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CMA1_HUMAN_22_247

Chymase [Peptidase S1 family. Granzyme subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (CMA1_HUMAN):D: Peptidase S1 (49:51, 66, 67, 102:107, 110, 151:154, 178:180, 197:201, 203, 217:222, 224, 228)49:51, 66, 67, 102:107, 110, 151:154, 178:180, 197:201, 203, 217:222, 224, 228

Full PDB list

1klt, 1nn6, 1pjp, 1t31, 2hvx, 3n7o, 3s0n, 4afq, 4afs, 4afu, 4afz, 4ag1, 4ag2, 4k2y, 4k5z, 4k60, 4k69, 4kp0 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
K
4
9
F
5
0
C
5
1
H
6
6
Y
1
0
2
N
1
0
3
T
1
0
4
S
1
0
5
T
1
0
6
L
1
0
7
D
1
1
0
D
1
8
0
S
1
9
7
A
1
9
8
F
1
9
9
K
2
0
0
G
2
0
1
S
2
0
3
V
2
1
7
S
2
1
8
Y
2
1
9
G
2
2
0
R
2
2
1
S
2
2
2
A
2
2
8
[1]1klt.a pms10 . . . . . . . . . . . . . . . . . * . . . . . . .
[1]1nn6.a none . . . . . . . . . . . . - . . . . . . . . . . . .
[1]1pjp.a AAPhph.0qe29 . . . * . . . . . . . . . . . . . * . . . . . . .
[1]1t31.a ohh49 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2hvx.a drx28 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3n7o.a n7o28 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3s0n.a 0bb27 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4afq.b RWTD-Y52 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4afz.a RWTD-Y,tar62 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4ag2.a na,RWT-Y45 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4ag2.b lmr,RWT-Y53 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4k2y.a es211 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4k5z.a 1p711 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4k60.a 1p811 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4k69.a 1p930 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4kp0.a kpk27 . . . . . . . . . . . . . . . . . . . . . . . . .

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
K
4
9
F
5
0
C
5
1
H
6
6
C
6
7
Y
1
0
2
N
1
0
3
T
1
0
4
S
1
0
5
T
1
0
6
L
1
0
7
D
1
1
0
R
1
5
1
T
1
5
2
G
1
5
3
V
1
5
4
F
1
7
8
R
1
7
9
D
1
8
0
S
1
9
7
A
1
9
8
F
1
9
9
K
2
0
0
G
2
0
1
S
2
0
3
V
2
1
7
S
2
1
8
Y
2
1
9
G
2
2
0
R
2
2
1
S
2
2
2
A
2
2
4
A
2
2
8
[1]1klt.a . . . * . * . . . . . . . . . . . . . . . . . . * . . . . . . . .
[1]1nn6.a . . . * . * . . . . . . . * . . . . . - . . * . * . . . . . . . .
[1]1pjp.a . . . * . . . . . . * . . . . . . . . . . . * . * . . . . . . . .
[1]1t31.a * . . . . * . . . . . . . . . . . . . . . . * . * . . . . . . . .
[1]2hvx.a . . . . . . . . . . . . . . . . . . . . . . * . * . . . . . . . .
[1]3n7o.a * . . . . . . . . . . . . . . . . . . . . . * . * . . . . . . . .
[1]3s0n.a . . . . . . . . . . . . . . . . . . . . . . * . * . . . . . . . .
[1]4afq.b . . . . . * . . . . . . . . . . . . . . . . . . * . . . . . . . .
[1]4afz.a . . . . . . . . . . * . . . . . . . . . . . . . * . . . . . . . .
[1]4ag2.a . . . . . . . . . . * . . . . . . . . . . . . . * . . . . . . . .
[1]4ag2.b . . . . . . . . . . * . . . . . . . . . . . . . * . . . . . . . .
[1]4k2y.a . . . . . * . . . . . . . . . . . . . . . . . . * . . . . . . . .
[1]4k5z.a . . . . . * . . . . . . . . . . . . . . . . * . * . . . . . . . .
[1]4k60.a . . . . . * . . . . . . . . . . . . . . . . . . * . . . . . . . .
[1]4k69.a . . . . . . . . . . * . . . . . . . . . . . . . * . . . . . . . .
[1]4kp0.a . . . . . . . . . . . . . . . . . . . . . . * . * . . . . . . . .

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

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pocketligand
≥10
9
8
7
6
5
4
3
2
1
0
1klt.a:pms
1nn6.a is apo
1pjp.a:AAPhph.0qe
1t31.a:ohh
2hvx.a:drx
3n7o.a:n7o
3s0n.a:0bb
4afq.b:RWTD-Y
4afz.a:RWTD-Y,tar
4ag2.a:RWT-Y,na
4ag2.b:RWT-Y,lmr
4k2y.a:es2
4k5z.a:1p7
4k60.a:1p8
4k69.a:1p9
4kp0.a:kpk
[1] 1klt.a
0.6
- 2.2 2.1 3.1 2.2 1.5 0.8 1.0 0.7 0.8 0 0.4 0.1 2.1 1.6
[1] 1nn6.a 2.6
-
3.5 3.1 5.0 4.6 2.1 1.7 2.3 1.5 2.1 2.3 2.3 2.0 3.2 3.6
[1] 1pjp.a 0.8 -
1.5
1.5 1.7 1.7 0 0.4 0.4 0.2 0.3 0.2 0.3 0.2 0.3 0.3
[1] 1t31.a 0.9 - 1.8
0.1
1.9 1.5 0.1 0 1.1 0.4 1.1 0 0.4 0.1 2.2 1.2
[1] 2hvx.a 0.6 - 1.3 0.9
0.7
0.5 0 0.8 0.8 0.5 0.6 0 0.3 0.1 0.7 0.5
[1] 3n7o.a 0.5 - 1.4 1.3 0.4
0
0 0.4 1.0 0.5 1.1 0.1 0.4 0.2 2.5 0.7
[1] 3s0n.a 0.7 - 1.4 1.0 1.4 1.3
0
0.2 0.2 0.2 0.2 0.1 0.3 0.2 0.2 0.1
[1] 4afq.b 0.8 - 1.4 0.5 2.2 1.9 0.2
0
0 0.3 0.3 0 0.4 0.1 1.2 0.5
[1] 4afz.a 0.8 - 1.8 0.9 2.2 1.7 0.1 0.1
0
0.5 0.8 0 0.4 0.1 1.0 0.3
[1] 4ag2.a 0.9 - 1.6 0.6 2.1 2.6 0.4 0.1 0.1
0
0 0.1 0.6 0.1 0.4 0.5
[1] 4ag2.b 1.0 - 1.6 0.6 2.2 2.6 0.5 0.3 0.2 0
0
0 0.3 0.1 0.6 0.7
[1] 4k2y.a 0.8 - 1.3 0.3 1.7 1.4 0 0.1 0.1 0.1 0.1
0
0.2 0 0.1 0.1
[1] 4k5z.a 1.0 - 1.5 0.8 1.8 1.6 0 0.4 0.3 0.1 0.3 0
0.1
0 0.1 0.3
[1] 4k60.a 1.0 - 1.5 0.5 1.9 1.5 0 0.2 0.3 0.1 0.2 0 0.1
0
0.1 0.2
[1] 4k69.a 0.5 - 1.1 0.7 2.0 1.7 0 0.2 0.3 0.2 0.3 0 0 0
0
0.2
[1] 4kp0.a 0.6 - 1.3 1.5 1.4 1.1 0 0.3 0.4 0.3 0.4 0.1 0.3 0.3 0.6
0.2
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (1 cluster)

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

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pocketpocket
≥1.
.9
.8
.7
.6
.5
.4
.3
.2
.1
.0
1klt.a
1nn6.a
1pjp.a
1t31.a
2hvx.a
3n7o.a
3s0n.a
4afq.b
4afz.a
4ag2.a
4ag2.b
4k2y.a
4k5z.a
4k60.a
4k69.a
4kp0.a
[1] 1klt.a
0
.21 .13 .13 .15 .18 .13 .10 .12 .14 .14 .10 .12 .11 .13 .15
[1] 1nn6.a .21
0
.14 .21 .17 .24 .15 .19 .23 .22 .22 .16 .16 .17 .18 .16
[1] 1pjp.a .13 .14
0
.15 .07 .13 .03 .10 .11 .10 .10 .08 .07 .09 .05 .05
[1] 1t31.a .13 .21 .15
0
.13 .08 .13 .08 .09 .16 .15 .11 .09 .10 .13 .13
[1] 2hvx.a .15 .17 .07 .13
0
.10 .04 .11 .12 .11 .11 .06 .07 .08 .07 .08
[1] 3n7o.a .18 .24 .13 .08 .10
0
.11 .13 .14 .17 .17 .15 .14 .15 .15 .11
[1] 3s0n.a .13 .15 .03 .13 .04 .11
0
.08 .10 .09 .08 .06 .06 .07 .04 .04
[1] 4afq.b .10 .19 .10 .08 .11 .13 .08
0
.05 .09 .08 .06 .08 .07 .08 .08
[1] 4afz.a .12 .23 .11 .09 .12 .14 .10 .05
0
.08 .08 .11 .11 .10 .08 .10
[1] 4ag2.a .14 .22 .10 .16 .11 .17 .09 .09 .08
0
.01 .11 .11 .10 .09 .11
[1] 4ag2.b .14 .22 .10 .15 .11 .17 .08 .08 .08 .01
0
.10 .11 .10 .08 .10
[1] 4k2y.a .10 .16 .08 .11 .06 .15 .06 .06 .11 .11 .10
0
.04 .02 .06 .09
[1] 4k5z.a .12 .16 .07 .09 .07 .14 .06 .08 .11 .11 .11 .04
0
.02 .06 .08
[1] 4k60.a .11 .17 .09 .10 .08 .15 .07 .07 .10 .10 .10 .02 .02
0
.06 .10
[1] 4k69.a .13 .18 .05 .13 .07 .15 .04 .08 .08 .09 .08 .06 .06 .06
0
.06
[1] 4kp0.a .15 .16 .05 .13 .08 .11 .04 .08 .10 .11 .10 .09 .08 .10 .06
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.3 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
1klt.a
1nn6.a
1pjp.a
1t31.a
2hvx.a
3n7o.a
3s0n.a
4afq.b
4afz.a
4ag2.a
4ag2.b
4k2y.a
4k5z.a
4k60.a
4k69.a
4kp0.a
[1] 1klt.a
0
3.8 0.6 0.4 0.6 0.5 0.6 0.4 0.4 0.7 0.7 0.5 0.6 0.6 0.6 0.6
[1] 1nn6.a 3.8
0
3.7 3.7 3.7 3.8 3.7 3.8 3.8 3.7 3.7 3.7 3.7 3.8 3.7 3.8
[1] 1pjp.a 0.6 3.7
0
0.7 0.2 0.7 0.2 0.7 0.7 0.4 0.4 0.4 0.4 0.5 0.3 0.4
[1] 1t31.a 0.4 3.7 0.7
0
0.7 0.4 0.7 0.4 0.5 0.8 0.8 0.7 0.8 0.7 0.7 0.8
[1] 2hvx.a 0.6 3.7 0.2 0.7
0
0.7 0.2 0.7 0.7 0.4 0.4 0.3 0.4 0.4 0.3 0.4
[1] 3n7o.a 0.5 3.8 0.7 0.4 0.7
0
0.7 0.6 0.6 0.8 0.8 0.7 0.7 0.7 0.7 0.7
[1] 3s0n.a 0.6 3.7 0.2 0.7 0.2 0.7
0
0.7 0.7 0.5 0.4 0.3 0.4 0.4 0.3 0.3
[1] 4afq.b 0.4 3.8 0.7 0.4 0.7 0.6 0.7
0
0.3 0.7 0.7 0.7 0.7 0.7 0.7 0.8
[1] 4afz.a 0.4 3.8 0.7 0.5 0.7 0.6 0.7 0.3
0
0.7 0.7 0.7 0.7 0.7 0.7 0.7
[1] 4ag2.a 0.7 3.7 0.4 0.8 0.4 0.8 0.5 0.7 0.7
0
0.2 0.5 0.5 0.5 0.4 0.5
[1] 4ag2.b 0.7 3.7 0.4 0.8 0.4 0.8 0.4 0.7 0.7 0.2
0
0.5 0.5 0.5 0.4 0.5
[1] 4k2y.a 0.5 3.7 0.4 0.7 0.3 0.7 0.3 0.7 0.7 0.5 0.5
0
0.2 0.2 0.2 0.4
[1] 4k5z.a 0.6 3.7 0.4 0.8 0.4 0.7 0.4 0.7 0.7 0.5 0.5 0.2
0
0.2 0.2 0.4
[1] 4k60.a 0.6 3.8 0.5 0.7 0.4 0.7 0.4 0.7 0.7 0.5 0.5 0.2 0.2
0
0.2 0.4
[1] 4k69.a 0.6 3.7 0.3 0.7 0.3 0.7 0.3 0.7 0.7 0.4 0.4 0.2 0.2 0.2
0
0.3
[1] 4kp0.a 0.6 3.8 0.4 0.8 0.4 0.7 0.3 0.8 0.7 0.5 0.5 0.4 0.4 0.4 0.3
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.6 Å)

Pockets (x) vs pockets (y) colored by RMSD of all site residue 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
1klt.a
1nn6.a
1pjp.a
1t31.a
2hvx.a
3n7o.a
3s0n.a
4afq.b
4afz.a
4ag2.a
4ag2.b
4k2y.a
4k5z.a
4k60.a
4k69.a
4kp0.a
[1] 1klt.a
0
4.3 1.0 1.1 1.0 1.1 1.8 1.1 1.2 1.8 1.7 1.7 1.8 1.8 1.7 1.1
[1] 1nn6.a 4.3
0
4.2 4.2 4.2 4.2 4.1 4.2 4.2 4.2 4.1 4.1 4.2 4.2 4.1 4.2
[1] 1pjp.a 1.0 4.2
0
1.0 0.4 1.0 0.8 1.3 1.4 1.2 1.1 0.9 0.9 1.1 1.0 0.7
[1] 1t31.a 1.1 4.2 1.0
0
0.9 0.8 1.4 1.3 1.3 1.5 1.4 1.4 1.5 1.6 1.5 1.1
[1] 2hvx.a 1.0 4.2 0.4 0.9
0
0.9 0.9 1.3 1.4 1.2 1.1 0.9 0.9 1.1 1.0 0.7
[1] 3n7o.a 1.1 4.2 1.0 0.8 0.9
0
1.4 1.4 1.3 1.5 1.4 1.4 1.5 1.6 1.5 1.0
[1] 3s0n.a 1.8 4.1 0.8 1.4 0.9 1.4
0
1.8 1.6 1.0 1.0 0.5 0.6 0.7 0.6 1.4
[1] 4afq.b 1.1 4.2 1.3 1.3 1.3 1.4 1.8
0
0.7 1.6 1.6 1.8 1.9 1.9 1.8 1.4
[1] 4afz.a 1.2 4.2 1.4 1.3 1.4 1.3 1.6 0.7
0
1.4 1.4 1.6 1.7 1.7 1.6 1.4
[1] 4ag2.a 1.8 4.2 1.2 1.5 1.2 1.5 1.0 1.6 1.4
0
0.3 1.0 1.1 1.2 1.0 1.4
[1] 4ag2.b 1.7 4.1 1.1 1.4 1.1 1.4 1.0 1.6 1.4 0.3
0
0.9 1.1 1.2 1.0 1.3
[1] 4k2y.a 1.7 4.1 0.9 1.4 0.9 1.4 0.5 1.8 1.6 1.0 0.9
0
0.3 0.5 0.5 1.4
[1] 4k5z.a 1.8 4.2 0.9 1.5 0.9 1.5 0.6 1.9 1.7 1.1 1.1 0.3
0
0.5 0.6 1.4
[1] 4k60.a 1.8 4.2 1.1 1.6 1.1 1.6 0.7 1.9 1.7 1.2 1.2 0.5 0.5
0
0.6 1.5
[1] 4k69.a 1.7 4.1 1.0 1.5 1.0 1.5 0.6 1.8 1.6 1.0 1.0 0.5 0.6 0.6
0
1.4
[1] 4kp0.a 1.1 4.2 0.7 1.1 0.7 1.0 1.4 1.4 1.4 1.4 1.3 1.4 1.4 1.5 1.4
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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