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AMP1_PLAFQ_195_1084

M1 family aminopeptidase [Peptidase M1 family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (AMP1_PLAFQ):R: Substrate binding (460:463)
304, 305, 317, 319, 320, 458, 459, 489, 492, 493, 496, 497, 500, 518, 519, 526, 571:576, 580, 997, 1034, 1037, 1038, 1073
304, 305, 317, 319, 320, 458:463, 489, 492, 493, 496, 497, 500, 518, 519, 526, 571:576, 580, 997, 1034, 1037, 1038, 1073
Metals (Me):Zn

Full PDB list

3ebg, 3ebh, 3ebi, 3q43, 3q44, 3t8v, 4j3b, 4k5l, 4k5m, 4k5n, 4k5o, 4k5p, 4r5t, 4r5v, 4r5x, 4x2u, 4zqt, 4zw3, 4zw5, 4zw6, 4zw7, 4zw8, 4zx3, 4zx4, 4zx5, 4zx6

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
L
3
0
4
T
3
0
5
Q
3
1
7
E
3
1
9
A
3
2
0
N
4
5
8
V
4
5
9
G
4
6
0
A
4
6
1
M
4
6
2
E
4
6
3
R
4
8
9
T
4
9
2
V
4
9
3
H
4
9
6
E
4
9
7
H
5
0
0
K
5
1
8
E
5
1
9
M
5
7
1
E
5
7
2
Y
5
7
5
Y
5
8
0
M
1
0
3
4
Q
1
0
3
8
N
1
0
7
3
[1]3ebg.a mg1 . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]3ebh.a bes22 . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]3ebi.a bey25 . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]3q43.a d6624 . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]3q44.a d5030 . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]3t8v.a btj40 . . . . . . . . . . . . . . . . . . . . A . . . . . Zn
[1]4j3b.a R12 . . . . . . P . . . . . . . . . . . . . . . . . . . Zn
[1]4k5l.a 19n14 . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]4k5m.a 1ov13 . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]4k5n.a 1ou16 . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]4k5o.a 1ot17 . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]4k5p.a 1os15 . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]4r5t.a r5t24 . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]4r5v.a r5v23 . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]4r5x.a r5x26 . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]4x2u.a tod24 . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]4zqt.a 4qp20 . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]4zw3.a 4s920 . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]4zw5.a 4sa25 . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]4zw6.a 4sy25 . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]4zw7.a 4sz28 . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]4zw8.a 4t229 . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]4zx3.a 4tk19 . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]4zx4.a 4tl27 . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]4zx5.a 4tm23 . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]4zx6.a 4u628 . . . . . . . . . . . . . . . . . . . - - . . . . . Zn

Legend

B backbone contact  S side chain contact  F BB + SCh
.
 no contact C covalent bond
X mutation to X * complex cases - deletion
M contact with cofactors/metals (if any)

Site contact map

[download in TSV format]
   
PDB.ch
A1 Me
L
3
0
4
T
3
0
5
Q
3
1
7
E
3
1
9
A
3
2
0
N
4
5
8
V
4
5
9
G
4
6
0
A
4
6
1
M
4
6
2
E
4
6
3
R
4
8
9
T
4
9
2
V
4
9
3
H
4
9
6
E
4
9
7
H
5
0
0
K
5
1
8
E
5
1
9
E
5
2
6
M
5
7
1
E
5
7
2
N
5
7
3
F
5
7
4
Y
5
7
5
T
5
7
6
Y
5
8
0
R
9
9
7
M
1
0
3
4
T
1
0
3
7
Q
1
0
3
8
N
1
0
7
3
[1]3ebg.a . . . . . . . . . . . . . . . . . . . . . * . . . . . . . . . . Zn
[1]3ebh.a . . . . . . . . . . . . . . . . . . . . . * . . . . . . * . . . Zn
[1]3ebi.a . . . . . . . . . . . . . . . . . . . . . * . . . . . . * . . . Zn
[1]3q43.a . . . . . . . . . . . . . . . . . . . . . * . . . . . . . . . . Zn
[1]3q44.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]3t8v.a . . . . . . . . . . . . . . . . . . . . . A . . . . . . . . . . Zn
[1]4j3b.a . . . . . . P . . . . . . . . . . . . . . * . . . . . . . . . . Zn
[1]4k5l.a . . . . . . * . . . . . . . . . . . . . . * . . . . . . . . . . Zn
[1]4k5m.a . . . . . . * . . . . . . . . . . . . . . * . . . . . . . . . . Zn
[1]4k5n.a . . . . . . . . . . . . . . . . . . . . . * . . . . . . . . . . Zn
[1]4k5o.a . . . . . . . . . . . . . . . . . . . . . * . . . . . . * . . . Zn
[1]4k5p.a . . . . . . . . . . . . . . . . . . . . . * . . . . . . * . . . Zn
[1]4r5t.a . . . . . . . . . . . . . . . . . . . . . * . . . . . . * . . . Zn
[1]4r5v.a . . . . . . . . . . . . . . . . . . . . . * . . . . . . * . . . Zn
[1]4r5x.a . . . . . . . . . * . . . . . . . . . . . * . . . . . . * . . . Zn
[1]4x2u.a . . . . . . . . . . . . . . . . . . . . . * . . . . . . * . . . Zn
[1]4zqt.a . . . . . . . . . . . . . . . . . . . . . * . . . . . . . . . . Zn
[1]4zw3.a . . . . . . . . . . . . . . . . . . . . . * . . . . . . * . . . Zn
[1]4zw5.a . . . . . . . . . . . . . . . . . . . . . * . . . . . . * . . . Zn
[1]4zw6.a . . . . . . . . . . . . . . . . . . . . . * . . . . . . * . . . Zn
[1]4zw7.a . . . . . . . . . . . . . . . . . . . . . * . . . . . . * . . . Zn
[1]4zw8.a . . . . . . . . . . . . . . . . . . . . . * . . . . . . * . . . Zn
[1]4zx3.a . . . . . . . . . . . . . . . . . . . . . * . . . . . . * . . . Zn
[1]4zx4.a . . . . . . . . . . . . . . . . . . . . . * . . . . . . * . . . Zn
[1]4zx5.a . . . . . . . . . . . . . . . . . . . . . * . . . . . . * . . . Zn
[1]4zx6.a . . . . . . . . . . . . . . . . . . . . - - . . . . . . * . . . Zn

Legend

B backbone contact  S side chain contact  F BB + SCh
.
 no contact C covalent bond
X X X X X  clash
X mutation to X * complex cases - deletion
M contact with cofactors/metals (if any)

Pocket-ligand steric compatibility

Ligands (x) vs pockets (y) colored by number of steric clashes

zoom: [−] [+]; [view as image]; [download as text]

pocketligand
≥10
9
8
7
6
5
4
3
2
1
0
3ebg.a:mg
3ebh.a:bes
3ebi.a:bey
3q43.a:d66
3q44.a:d50
3t8v.a:btj
4j3b.a:R
4k5l.a:19n
4k5m.a:1ov
4k5n.a:1ou
4k5o.a:1ot
4k5p.a:1os
4r5t.a:r5t
4r5v.a:r5v
4r5x.a:r5x
4x2u.a:tod
4zqt.a:4qp
4zw3.a:4s9
4zw5.a:4sa
4zw6.a:4sy
4zw7.a:4sz
4zw8.a:4t2
4zx3.a:4tk
4zx4.a:4tl
4zx5.a:4tm
4zx6.a:4u6
[1] 3ebg.a
0
0.2 0.2 0.1 2.9 0.2 0.1 0.2 0.2 0.3 0.4 0.1 0.2 0.2 0.1 0.5 0.4 0.2 0.2 0.3 0.3 0.6 0.2 0.3 0.3 1.4
[1] 3ebh.a 0
0.1
0.6 0.1 4.3 1.7 0.7 0.5 0.4 0.5 0.3 0.7 0.5 0.5 0.3 0.5 0.3 0.2 0.3 0.3 0.3 0.4 0.1 0.3 0.5 1.7
[1] 3ebi.a 0 0.1
0.2
0.5 3.7 1.7 0.1 0.4 0 0.9 0.3 0 0.4 0.5 0.3 0.5 0.3 0.1 0.2 0.2 0.6 0.4 0.1 0.5 0.5 1.9
[1] 3q43.a 0 0.2 0.5
0.1
1.6 0.1 0.2 0.2 0.1 0.2 0.2 0.5 0.4 0.2 0.2 0.5 0.3 0.1 0.1 0.1 0.2 0.3 0.1 0.2 0.4 0.3
[1] 3q44.a 0 0.2 0.4 0
0
0.3 0.3 0.3 0.2 0.2 0.3 0.4 0.4 0.3 0.3 0.5 0.4 0.1 0.4 0.2 0.2 0.3 0.3 0.5 0.5 0.4
[1] 3t8v.a 0 0.2 0.4 0 1.7
0
0.2 0.2 0.2 0.3 0.2 0.4 0.5 0.2 0.1 0.5 0.3 0.1 0.1 0.2 0.4 0.3 0.1 0.3 0.1 0.7
[1] 4j3b.a 0 0.4 0.4 0.5 5.0 1.0
0.1
0.4 0.1 0.8 0.6 0.5 0.9 0.5 0.3 0.5 0.5 0.3 0.7 0.8 1.2 0.7 0.2 1.2 0.6 1.6
[1] 4k5l.a 0 0.3 0.4 0.2 3.1 0.7 0
0.1
0 0.2 0 0 0.4 0.4 0.5 2.6 0.4 0.3 0.3 0.4 0.3 0.3 0.2 0.3 0.2 1.6
[1] 4k5m.a 0 0.5 0.4 0.3 2.9 1.1 0.1 0.1
0.2
0.3 0.3 0.3 0.3 0.3 0.4 2.5 0.6 0.4 0.4 0.5 0.4 0.6 0.3 0.4 0.3 1.3
[1] 4k5n.a 0 0.1 0.2 0.1 2.8 0.2 0 0 0
0.1
0 0 0.1 0.2 0.1 0.3 0.3 0 0.2 0.1 0.2 0.3 0.1 0.2 0.2 1.1
[1] 4k5o.a 0 0.2 0.3 0.1 3.0 1.1 0.2 0.1 0 0.3
0.1
0.2 0.1 0.2 0.1 0.4 0.4 0 0.1 0.1 0.1 0.3 0.1 0.1 0.2 1.1
[1] 4k5p.a 0 0.2 0.3 0.1 3.1 1.1 0.2 0.1 0.1 0.2 0.2
0.1
0.2 0.1 0.1 0.3 0.3 0.2 0.3 0.3 0.3 0.4 0.2 0.2 0.2 1.3
[1] 4r5t.a 0 0.1 0.2 0.1 3.3 1.0 0 0 0 0 0.2 0.2
0
0.1 0.1 0.4 0.2 0 0.1 0.1 0.1 0.2 0.1 0.1 0.1 1.1
[1] 4r5v.a 0 0.5 0.5 0.5 3.0 1.5 0.3 0.4 0.4 0.6 0.7 0.7 0.1
0.1
0 0.5 0.6 0.1 0.3 0.1 0.2 0.3 0.1 0.1 0.1 1.2
[1] 4r5x.a 0 0.3 0.4 0.5 2.6 1.5 0.1 0.3 0.4 0.6 0.8 0.8 0.1 0.1
0.1
0.3 0.6 0.2 0.4 0.3 0.3 0.5 0.3 0.4 0.2 1.5
[1] 4x2u.a 0 0.1 0.4 0 3.4 0.9 0.1 0.1 0.1 0.2 0.1 0 0.2 0.2 0.2
0.2
0.2 0 0.2 0.1 0.2 0.2 0.1 0.2 0.1 1.0
[1] 4zqt.a 0 0.1 0.3 0 2.6 0.3 0 0 0 0 0.1 0.1 0 0.2 0.1 0.3
0.2
0 0.1 0.1 0.1 0.4 0 0 0 1.0
[1] 4zw3.a 0 0.2 0.3 0.1 2.4 1.3 0.1 0 0 0.3 0.1 0.2 0.2 0.2 0.1 0.4 0.3
0
0.2 0.2 0.3 0.5 0.1 0.2 0.1 0.7
[1] 4zw5.a 0 0.1 0.4 0.2 4.1 1.4 0.2 0.4 0.1 0.6 0.3 0.5 0.3 0.5 0.2 0.4 0.3 0.1
0.1
0.2 0.2 0.5 0.1 0.1 0.2 1.8
[1] 4zw6.a 0 0.2 0.3 0.1 3.3 1.6 0.2 0.5 0.2 0.3 0 0.2 0.3 0.3 0.2 0.4 0.3 0.1 0.1
0.1
0.2 0.3 0.1 0.1 0.2 1.4
[1] 4zw7.a 0 0.1 0.3 0.2 4.0 1.5 0.2 0.4 0.2 0.6 0.3 0.6 0.3 0.5 0.2 0.4 0.3 0.1 0.1 0.2
0.2
0.6 0.1 0.1 0.2 1.8
[1] 4zw8.a 0 0.1 0.3 0.2 2.6 1.5 0.2 0.3 0.2 0.4 0 0.5 0.3 0.3 0.3 0.4 0.3 0 0.1 0.1 0.2
0.4
0.1 0.1 0.2 0.9
[1] 4zx3.a 0 0.2 0.3 0.1 3.2 1.5 0.1 0 0 0.4 0.1 0.3 0.2 0.1 0.1 0.5 0.3 0 0.2 0.2 0.2 0.4
0.1
0.1 0.2 0.7
[1] 4zx4.a 0 0.2 0.3 0.3 3.7 1.9 0.2 0.4 0.3 0.5 0.3 0.4 0.2 0.5 0.2 0.5 0.3 0 0.1 0.1 0.1 0.2 0.1
0.1
0.2 1.5
[1] 4zx5.a 0 0.2 0.3 0.1 2.9 1.2 0.1 0 0 0.2 0.3 0.3 0.1 0.2 0 0.4 0.3 0 0.2 0.1 0.1 0.3 0.1 0.1
0.1
0.8
[1] 4zx6.a 0 0.2 0.3 0.1 0.2 1.3 0.1 0.1 0.1 0.2 0.1 0.3 0.1 0.1 0.1 0.3 0.3 0 0 0 0.1 0.2 0 0 0
0
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (1 cluster)

Pockets (x) vs pockets (y) colored by ligand clash profile difference

zoom: [−] [+]; [view as image]; [download as text]

pocketpocket
≥1.
.9
.8
.7
.6
.5
.4
.3
.2
.1
.0
3ebg.a
3ebh.a
3ebi.a
3q43.a
3q44.a
3t8v.a
4j3b.a
4k5l.a
4k5m.a
4k5n.a
4k5o.a
4k5p.a
4r5t.a
4r5v.a
4r5x.a
4x2u.a
4zqt.a
4zw3.a
4zw5.a
4zw6.a
4zw7.a
4zw8.a
4zx3.a
4zx4.a
4zx5.a
4zx6.a
[1] 3ebg.a
0
.12 .08 .07 .12 .06 .10 .10 .10 .02 .05 .04 .06 .07 .08 .05 .03 .06 .08 .07 .09 .06 .07 .09 .06 .14
[1] 3ebh.a .12
0
.07 .14 .18 .14 .12 .19 .18 .12 .08 .08 .08 .11 .12 .07 .12 .09 .05 .05 .05 .07 .06 .05 .07 .16
[1] 3ebi.a .08 .07
0
.13 .18 .12 .10 .15 .14 .09 .06 .05 .05 .07 .09 .04 .09 .06 .04 .03 .05 .05 .04 .03 .05 .12
[1] 3q43.a .07 .14 .13
0
.06 .02 .13 .15 .14 .06 .09 .10 .10 .09 .09 .11 .07 .07 .13 .12 .14 .09 .11 .13 .09 .12
[1] 3q44.a .12 .18 .18 .06
0
.08 .18 .19 .19 .11 .14 .15 .15 .14 .15 .15 .12 .12 .18 .16 .19 .14 .15 .18 .14 .07
[1] 3t8v.a .06 .14 .12 .02 .08
0
.13 .14 .13 .06 .09 .08 .10 .09 .09 .09 .07 .06 .12 .11 .13 .08 .10 .12 .08 .11
[1] 4j3b.a .10 .12 .10 .13 .18 .13
0
.17 .17 .11 .13 .13 .11 .13 .15 .10 .11 .14 .11 .12 .12 .14 .12 .12 .13 .21
[1] 4k5l.a .10 .19 .15 .15 .19 .14 .17
0
.04 .10 .13 .12 .14 .14 .16 .13 .10 .14 .17 .15 .18 .15 .14 .17 .13 .21
[1] 4k5m.a .10 .18 .14 .14 .19 .13 .17 .04
0
.09 .12 .12 .13 .13 .12 .13 .10 .12 .14 .14 .16 .12 .13 .15 .12 .19
[1] 4k5n.a .02 .12 .09 .06 .11 .06 .11 .10 .09
0
.05 .04 .07 .06 .07 .06 .02 .06 .08 .08 .10 .06 .08 .09 .07 .13
[1] 4k5o.a .05 .08 .06 .09 .14 .09 .13 .13 .12 .05
0
.02 .03 .04 .05 .04 .05 .04 .05 .05 .07 .04 .04 .06 .03 .12
[1] 4k5p.a .04 .08 .05 .10 .15 .08 .13 .12 .12 .04 .02
0
.03 .05 .05 .02 .06 .04 .05 .04 .07 .04 .04 .06 .03 .12
[1] 4r5t.a .06 .08 .05 .10 .15 .10 .11 .14 .13 .07 .03 .03
0
.05 .05 .02 .06 .05 .05 .03 .06 .06 .04 .04 .03 .13
[1] 4r5v.a .07 .11 .07 .09 .14 .09 .13 .14 .13 .06 .04 .05 .05
0
.03 .05 .06 .04 .08 .06 .08 .05 .05 .07 .04 .12
[1] 4r5x.a .08 .12 .09 .09 .15 .09 .15 .16 .12 .07 .05 .05 .05 .03
0
.06 .07 .04 .08 .08 .09 .05 .07 .08 .05 .12
[1] 4x2u.a .05 .07 .04 .11 .15 .09 .10 .13 .13 .06 .04 .02 .02 .05 .06
0
.06 .05 .04 .03 .05 .05 .04 .04 .03 .12
[1] 4zqt.a .03 .12 .09 .07 .12 .07 .11 .10 .10 .02 .05 .06 .06 .06 .07 .06
0
.06 .09 .07 .09 .06 .07 .09 .06 .13
[1] 4zw3.a .06 .09 .06 .07 .12 .06 .14 .14 .12 .06 .04 .04 .05 .04 .04 .05 .06
0
.06 .05 .08 .02 .04 .07 .03 .08
[1] 4zw5.a .08 .05 .04 .13 .18 .12 .11 .17 .14 .08 .05 .05 .05 .08 .08 .04 .09 .06
0
.04 .02 .06 .05 .04 .04 .14
[1] 4zw6.a .07 .05 .03 .12 .16 .11 .12 .15 .14 .08 .05 .04 .03 .06 .08 .03 .07 .05 .04
0
.04 .02 .02 .02 .03 .11
[1] 4zw7.a .09 .05 .05 .14 .19 .13 .12 .18 .16 .10 .07 .07 .06 .08 .09 .05 .09 .08 .02 .04
0
.07 .05 .03 .05 .14
[1] 4zw8.a .06 .07 .05 .09 .14 .08 .14 .15 .12 .06 .04 .04 .06 .05 .05 .05 .06 .02 .06 .02 .07
0
.03 .04 .04 .09
[1] 4zx3.a .07 .06 .04 .11 .15 .10 .12 .14 .13 .08 .04 .04 .04 .05 .07 .04 .07 .04 .05 .02 .05 .03
0
.03 .02 .11
[1] 4zx4.a .09 .05 .03 .13 .18 .12 .12 .17 .15 .09 .06 .06 .04 .07 .08 .04 .09 .07 .04 .02 .03 .04 .03
0
.04 .13
[1] 4zx5.a .06 .07 .05 .09 .14 .08 .13 .13 .12 .07 .03 .03 .03 .04 .05 .03 .06 .03 .04 .03 .05 .04 .02 .04
0
.11
[1] 4zx6.a .14 .16 .12 .12 .07 .11 .21 .21 .19 .13 .12 .12 .13 .12 .12 .12 .13 .08 .14 .11 .14 .09 .11 .13 .11
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.8 Å)

Pockets (x) vs pockets (y) colored by RMSD of site residue backbone atoms

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pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
3ebg.a
3ebh.a
3ebi.a
3q43.a
3q44.a
3t8v.a
4j3b.a
4k5l.a
4k5m.a
4k5n.a
4k5o.a
4k5p.a
4r5t.a
4r5v.a
4r5x.a
4x2u.a
4zqt.a
4zw3.a
4zw5.a
4zw6.a
4zw7.a
4zw8.a
4zx3.a
4zx4.a
4zx5.a
4zx6.a
[1] 3ebg.a
0
0.2 0.2 0.4 1.2 0.3 0.4 0.4 0.4 0.2 0.2 0.4 0.3 0.3 0.3 0.2 0.2 0.2 0.3 0.2 0.3 0.3 0.2 0.2 0.2 0.2
[1] 3ebh.a 0.2
0
0.3 0.5 1.2 0.4 0.4 0.5 0.5 0.3 0.2 0.4 0.4 0.3 0.3 0.3 0.2 0.3 0.2 0.2 0.2 0.3 0.3 0.2 0.3 0.3
[1] 3ebi.a 0.2 0.3
0
0.3 1.1 0.3 0.3 0.4 0.4 0.3 0.3 0.4 0.4 0.4 0.3 0.2 0.3 0.2 0.4 0.3 0.4 0.4 0.2 0.3 0.2 0.3
[1] 3q43.a 0.4 0.5 0.3
0
1.0 0.2 0.4 0.6 0.5 0.5 0.5 0.6 0.5 0.5 0.5 0.3 0.4 0.3 0.6 0.4 0.6 0.6 0.3 0.5 0.3 0.3
[1] 3q44.a 1.2 1.2 1.1 1.0
0
1.0 1.1 1.2 1.2 1.2 1.3 1.3 1.2 1.2 1.2 1.1 1.2 1.1 1.3 1.2 1.3 1.3 1.1 1.2 1.1 0.8
[1] 3t8v.a 0.3 0.4 0.3 0.2 1.0
0
0.4 0.5 0.5 0.4 0.5 0.5 0.5 0.5 0.4 0.2 0.3 0.2 0.5 0.3 0.5 0.5 0.3 0.4 0.2 0.2
[1] 4j3b.a 0.4 0.4 0.3 0.4 1.1 0.4
0
0.6 0.5 0.5 0.5 0.6 0.5 0.5 0.5 0.3 0.4 0.3 0.5 0.5 0.5 0.6 0.3 0.5 0.3 0.4
[1] 4k5l.a 0.4 0.5 0.4 0.6 1.2 0.5 0.6
0
0.1 0.4 0.4 0.5 0.5 0.5 0.5 0.5 0.4 0.4 0.5 0.4 0.5 0.5 0.5 0.4 0.5 0.5
[1] 4k5m.a 0.4 0.5 0.4 0.5 1.2 0.5 0.5 0.1
0
0.5 0.4 0.5 0.5 0.5 0.5 0.4 0.4 0.4 0.5 0.4 0.5 0.5 0.4 0.4 0.4 0.4
[1] 4k5n.a 0.2 0.3 0.3 0.5 1.2 0.4 0.5 0.4 0.5
0
0.2 0.3 0.3 0.3 0.3 0.3 0.2 0.3 0.3 0.2 0.3 0.3 0.3 0.3 0.3 0.2
[1] 4k5o.a 0.2 0.2 0.3 0.5 1.3 0.5 0.5 0.4 0.4 0.2
0
0.3 0.3 0.3 0.3 0.3 0.2 0.3 0.2 0.2 0.2 0.2 0.4 0.2 0.3 0.2
[1] 4k5p.a 0.4 0.4 0.4 0.6 1.3 0.5 0.6 0.5 0.5 0.3 0.3
0
0.2 0.2 0.2 0.4 0.3 0.4 0.3 0.3 0.3 0.3 0.5 0.3 0.4 0.4
[1] 4r5t.a 0.3 0.4 0.4 0.5 1.2 0.5 0.5 0.5 0.5 0.3 0.3 0.2
0
0.2 0.2 0.3 0.3 0.4 0.3 0.3 0.3 0.3 0.4 0.3 0.4 0.3
[1] 4r5v.a 0.3 0.3 0.4 0.5 1.2 0.5 0.5 0.5 0.5 0.3 0.3 0.2 0.2
0
0.2 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.4 0.3 0.3 0.3
[1] 4r5x.a 0.3 0.3 0.3 0.5 1.2 0.4 0.5 0.5 0.5 0.3 0.3 0.2 0.2 0.2
0
0.3 0.3 0.3 0.3 0.3 0.3 0.4 0.3 0.3 0.3 0.3
[1] 4x2u.a 0.2 0.3 0.2 0.3 1.1 0.2 0.3 0.5 0.4 0.3 0.3 0.4 0.3 0.3 0.3
0
0.2 0.1 0.4 0.2 0.3 0.4 0.2 0.3 0.2 0.2
[1] 4zqt.a 0.2 0.2 0.3 0.4 1.2 0.3 0.4 0.4 0.4 0.2 0.2 0.3 0.3 0.3 0.3 0.2
0
0.2 0.3 0.2 0.3 0.2 0.3 0.2 0.2 0.2
[1] 4zw3.a 0.2 0.3 0.2 0.3 1.1 0.2 0.3 0.4 0.4 0.3 0.3 0.4 0.4 0.3 0.3 0.1 0.2
0
0.4 0.2 0.4 0.4 0.1 0.3 0.2 0.2
[1] 4zw5.a 0.3 0.2 0.4 0.6 1.3 0.5 0.5 0.5 0.5 0.3 0.2 0.3 0.3 0.3 0.3 0.4 0.3 0.4
0
0.2 0.1 0.2 0.4 0.1 0.4 0.3
[1] 4zw6.a 0.2 0.2 0.3 0.4 1.2 0.3 0.5 0.4 0.4 0.2 0.2 0.3 0.3 0.3 0.3 0.2 0.2 0.2 0.2
0
0.2 0.2 0.3 0.2 0.2 0.2
[1] 4zw7.a 0.3 0.2 0.4 0.6 1.3 0.5 0.5 0.5 0.5 0.3 0.2 0.3 0.3 0.3 0.3 0.3 0.3 0.4 0.1 0.2
0
0.3 0.4 0.1 0.4 0.3
[1] 4zw8.a 0.3 0.3 0.4 0.6 1.3 0.5 0.6 0.5 0.5 0.3 0.2 0.3 0.3 0.3 0.4 0.4 0.2 0.4 0.2 0.2 0.3
0
0.5 0.2 0.4 0.2
[1] 4zx3.a 0.2 0.3 0.2 0.3 1.1 0.3 0.3 0.5 0.4 0.3 0.4 0.5 0.4 0.4 0.3 0.2 0.3 0.1 0.4 0.3 0.4 0.5
0
0.3 0.2 0.2
[1] 4zx4.a 0.2 0.2 0.3 0.5 1.2 0.4 0.5 0.4 0.4 0.3 0.2 0.3 0.3 0.3 0.3 0.3 0.2 0.3 0.1 0.2 0.1 0.2 0.3
0
0.3 0.2
[1] 4zx5.a 0.2 0.3 0.2 0.3 1.1 0.2 0.3 0.5 0.4 0.3 0.3 0.4 0.4 0.3 0.3 0.2 0.2 0.2 0.4 0.2 0.4 0.4 0.2 0.3
0
0.1
[1] 4zx6.a 0.2 0.3 0.3 0.3 0.8 0.2 0.4 0.5 0.4 0.2 0.2 0.4 0.3 0.3 0.3 0.2 0.2 0.2 0.3 0.2 0.3 0.2 0.2 0.2 0.1
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.3 Å)

Pockets (x) vs pockets (y) colored by RMSD of all site residue atoms

zoom: [−] [+]; [view as image]; [download as text]

pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
3ebg.a
3ebh.a
3ebi.a
3q43.a
3q44.a
3t8v.a
4j3b.a
4k5l.a
4k5m.a
4k5n.a
4k5o.a
4k5p.a
4r5t.a
4r5v.a
4r5x.a
4x2u.a
4zqt.a
4zw3.a
4zw5.a
4zw6.a
4zw7.a
4zw8.a
4zx3.a
4zx4.a
4zx5.a
4zx6.a
[1] 3ebg.a
0
0.6 0.9 0.9 1.4 0.5 0.9 0.7 0.9 0.3 0.4 0.4 0.5 0.6 0.7 0.6 0.6 0.9 0.7 0.8 0.6 0.7 1.0 0.7 0.6 0.6
[1] 3ebh.a 0.6
0
0.9 1.1 1.8 0.8 1.1 0.9 1.1 0.8 0.5 0.6 0.7 0.8 0.8 0.7 0.7 0.9 0.6 0.6 0.3 0.4 1.0 0.5 0.5 0.5
[1] 3ebi.a 0.9 0.9
0
0.7 1.9 0.9 0.8 1.1 0.9 1.0 0.9 1.0 1.0 1.0 0.8 1.0 1.0 0.4 1.0 1.0 0.9 1.0 0.6 1.0 0.6 0.8
[1] 3q43.a 0.9 1.1 0.7
0
1.5 0.8 0.6 1.1 0.9 1.0 1.1 1.1 1.0 1.1 0.9 0.9 0.9 0.6 1.1 1.1 1.1 1.1 0.7 1.1 0.7 1.0
[1] 3q44.a 1.4 1.8 1.9 1.5
0
1.3 1.8 1.6 1.8 1.5 1.6 1.8 1.7 1.5 1.6 1.6 1.4 1.6 1.8 1.7 1.8 1.8 1.9 1.8 1.6 1.4
[1] 3t8v.a 0.5 0.8 0.9 0.8 1.3
0
0.9 0.8 1.0 0.6 0.6 0.6 0.5 0.6 0.7 0.6 0.6 0.8 0.8 0.8 0.8 0.8 0.9 0.7 0.7 0.6
[1] 4j3b.a 0.9 1.1 0.8 0.6 1.8 0.9
0
1.1 0.9 1.0 1.0 1.1 1.1 1.0 0.9 0.9 0.9 0.6 1.0 1.0 1.1 1.2 0.7 1.0 0.8 1.1
[1] 4k5l.a 0.7 0.9 1.1 1.1 1.6 0.8 1.1
0
0.8 0.7 0.7 0.8 0.8 0.9 0.9 0.9 0.9 1.1 0.9 1.0 0.9 0.9 1.1 0.9 0.9 0.8
[1] 4k5m.a 0.9 1.1 0.9 0.9 1.8 1.0 0.9 0.8
0
1.0 1.0 1.0 1.1 1.1 0.9 1.1 1.1 0.9 1.1 1.2 1.1 1.1 0.9 1.1 0.8 1.0
[1] 4k5n.a 0.3 0.8 1.0 1.0 1.5 0.6 1.0 0.7 1.0
0
0.4 0.5 0.6 0.7 0.8 0.7 0.7 0.9 0.8 0.8 0.7 0.8 1.1 0.8 0.7 0.6
[1] 4k5o.a 0.4 0.5 0.9 1.1 1.6 0.6 1.0 0.7 1.0 0.4
0
0.2 0.4 0.6 0.7 0.6 0.6 0.9 0.7 0.7 0.5 0.5 1.0 0.6 0.5 0.4
[1] 4k5p.a 0.4 0.6 1.0 1.1 1.8 0.6 1.1 0.8 1.0 0.5 0.2
0
0.5 0.5 0.7 0.7 0.6 0.9 0.7 0.8 0.5 0.6 1.0 0.6 0.6 0.5
[1] 4r5t.a 0.5 0.7 1.0 1.0 1.7 0.5 1.1 0.8 1.1 0.6 0.4 0.5
0
0.4 0.6 0.7 0.5 0.9 0.7 0.8 0.7 0.7 1.0 0.7 0.7 0.6
[1] 4r5v.a 0.6 0.8 1.0 1.1 1.5 0.6 1.0 0.9 1.1 0.7 0.6 0.5 0.4
0
0.6 0.5 0.5 0.9 0.6 0.7 0.7 0.7 0.9 0.5 0.7 0.6
[1] 4r5x.a 0.7 0.8 0.8 0.9 1.6 0.7 0.9 0.9 0.9 0.8 0.7 0.7 0.6 0.6
0
0.8 0.8 0.7 0.8 0.8 0.8 0.8 0.7 0.7 0.6 0.7
[1] 4x2u.a 0.6 0.7 1.0 0.9 1.6 0.6 0.9 0.9 1.1 0.7 0.6 0.7 0.7 0.5 0.8
0
0.4 0.8 0.5 0.6 0.7 0.8 0.9 0.5 0.7 0.7
[1] 4zqt.a 0.6 0.7 1.0 0.9 1.4 0.6 0.9 0.9 1.1 0.7 0.6 0.6 0.5 0.5 0.8 0.4
0
0.9 0.5 0.6 0.6 0.7 0.9 0.5 0.7 0.7
[1] 4zw3.a 0.9 0.9 0.4 0.6 1.6 0.8 0.6 1.1 0.9 0.9 0.9 0.9 0.9 0.9 0.7 0.8 0.9
0
0.9 0.9 0.9 0.9 0.5 0.8 0.5 0.9
[1] 4zw5.a 0.7 0.6 1.0 1.1 1.8 0.8 1.0 0.9 1.1 0.8 0.7 0.7 0.7 0.6 0.8 0.5 0.5 0.9
0
0.4 0.5 0.6 0.9 0.3 0.7 0.7
[1] 4zw6.a 0.8 0.6 1.0 1.1 1.7 0.8 1.0 1.0 1.2 0.8 0.7 0.8 0.8 0.7 0.8 0.6 0.6 0.9 0.4
0
0.6 0.7 0.9 0.4 0.6 0.7
[1] 4zw7.a 0.6 0.3 0.9 1.1 1.8 0.8 1.1 0.9 1.1 0.7 0.5 0.5 0.7 0.7 0.8 0.7 0.6 0.9 0.5 0.6
0
0.4 1.0 0.5 0.5 0.5
[1] 4zw8.a 0.7 0.4 1.0 1.1 1.8 0.8 1.2 0.9 1.1 0.8 0.5 0.6 0.7 0.7 0.8 0.8 0.7 0.9 0.6 0.7 0.4
0
1.0 0.6 0.5 0.5
[1] 4zx3.a 1.0 1.0 0.6 0.7 1.9 0.9 0.7 1.1 0.9 1.1 1.0 1.0 1.0 0.9 0.7 0.9 0.9 0.5 0.9 0.9 1.0 1.0
0
0.8 0.6 0.9
[1] 4zx4.a 0.7 0.5 1.0 1.1 1.8 0.7 1.0 0.9 1.1 0.8 0.6 0.6 0.7 0.5 0.7 0.5 0.5 0.8 0.3 0.4 0.5 0.6 0.8
0
0.6 0.6
[1] 4zx5.a 0.6 0.5 0.6 0.7 1.6 0.7 0.8 0.9 0.8 0.7 0.5 0.6 0.7 0.7 0.6 0.7 0.7 0.5 0.7 0.6 0.5 0.5 0.6 0.6
0
0.3
[1] 4zx6.a 0.6 0.5 0.8 1.0 1.4 0.6 1.1 0.8 1.0 0.6 0.4 0.5 0.6 0.6 0.7 0.7 0.7 0.9 0.7 0.7 0.5 0.5 0.9 0.6 0.3
0
[Binding site full-atom RMSD matrix]







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