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ALR_GEOSE_1_388

Alanine racemase [Alanine racemase family]

Composition of the binding site

Protein chains homodimer
A1 (ALR_GEOSE):37, 39, 43, 85, 129, 136, 164, 166, 202:204, 219:223, 229, 35437, 39, 43, 85, 129, 136, 164, 166, 202:204, 219:223, 229, 354
A2 (ALR_GEOSE):265, 284, 285, 311:313265, 284, 285, 311:313

Full PDB list

1bd0, 1epv, 1ftx, 1l6f, 1l6g, 1niu, 1sft, 1xqk, 1xql, 2sfp, 3uw6, 4ils (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 A2
V
3
7
K
3
9
Y
4
3
L
8
5
K
1
2
9
R
1
3
6
Y
1
6
4
H
1
6
6
N
2
0
3
S
2
0
4
R
2
1
9
G
2
2
1
I
2
2
2
Y
3
5
4
Y
2
6
5
Y
2
8
4
C
3
1
1
M
3
1
2
[1]1bd0.a in522 . . . . . . . . . . . . . . . . . .
[1]1epv.b dcs22 . . . . * . . . . . . . . . . . . .
[1]1ftx.a epc22 . . . . * . . . . . . . . . . . . .
[1]1l6f.a pp321 . . . . * . . . . . . . . . . . . .
[1]1l6g.a pdd21 . . . . * . . . . . . . . . . . . .
[1]1sft.a plp15 . * . . . . . . . . . . . . . . . .
[1]1xqk.a pmh22 . . . . * . . . . . . . . . F . . .
[1]1xql.a 4ax,plp,pmh,pmp60 . . . . * . . . . . . . . . F . . .
[1]2sfp.a plp15 . * . . * . . . . . . . . . . . . .
[1]3uw6.b none S C . T Y S W W . . Q . . . F . L G
[1]4ils.a none S C . T Y - W W . . Q . . . . . L .
[1]4ils.b none S C . T Y S W W . . Q . . . - . L .

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

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PDB.ch
A1 A2
V
3
7
K
3
9
Y
4
3
L
8
5
K
1
2
9
R
1
3
6
Y
1
6
4
H
1
6
6
A
2
0
2
N
2
0
3
S
2
0
4
R
2
1
9
F
2
2
0
G
2
2
1
I
2
2
2
A
2
2
3
P
2
2
9
Y
3
5
4
Y
2
6
5
Y
2
8
4
A
2
8
5
C
3
1
1
M
3
1
2
D
3
1
3
[1]1bd0.a . . . . . . . . . . . . . . . . . . . . . . . .
[1]1epv.b . . . . * . . . . . . . . . . . . . . . . . . .
[1]1ftx.a . . . . * . . . . . . . . . . . . . . . . . . .
[1]1l6f.a . . . . * . . . . . . . . . . . . . . . . . . .
[1]1l6g.a . . . . * . . . . . . . . . . . . . . . . . . .
[1]1sft.a . * . . . . . . . . . . . . . . . . . . . . . .
[1]1xqk.a . . . . * . . . . . . . . . . . . . F . . . . .
[1]1xql.a . . . . * . . . . . . . . . . . . . F . . . . .
[1]2sfp.a . * . . * . . . . . . . . . . . . . . . . . . .
[1]3uw6.b S C . T Y S W W . . . Q . . . . . . F . K L G .
[1]4ils.a S C . T Y - W W . . . Q . . . . - . . . K L . .
[1]4ils.b S C . T Y S W W . . . Q . . . . - . - . K L * .

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
1bd0.a:in5
1epv.b:dcs
1ftx.a:epc
1l6f.a:pp3
1l6g.a:pdd
1sft.a:plp
1xqk.a:pmh
1xql.a:4ax,plp,pmh,pmp
2sfp.a:plp
3uw6.b is apo
4ils.a is apo
4ils.b is apo
[1] 1bd0.a
0.1
0.6 0.4 0.1 0.1 0.1 0.1 0.2 0.3 - - -
[1] 1epv.b 0.8
0.8
1.1 0.5 0.6 0.5 0.5 1.0 0.6 - - -
[1] 1ftx.a 0.3 0.6
0.6
0.2 0.1 0.1 0.1 0.3 0.2 - - -
[1] 1l6f.a 0.5 0.5 0.7
0
0.1 0.2 0.2 0.5 0.6 - - -
[1] 1l6g.a 0.7 0.8 0.8 0.1
0.3
0.2 0.2 0.7 0.6 - - -
[1] 1sft.a 0.6 0.9 1.3 0.3 0.7
0.9
0.7 1.2 0.8 - - -
[1] 1xqk.a 0.6 0.7 0.9 0.3 0.3 0.2
0.3
0.5 0.8 - - -
[1] 1xql.a 0.6 0.5 0.8 0.2 0.2 0.1 0.3
0.4
0.4 - - -
[1] 2sfp.a 0.8 1.3 1.4 0.2 0.5 0.4 0.7 0.9
0.6
- - -
[1] 3uw6.b 1.2 1.0 1.5 1.3 1.0 0.7 1.4 2.1 0.8
-
- -
[1] 4ils.a 1.9 1.2 2.0 1.4 1.3 1.0 1.4 2.1 1.1 -
-
-
[1] 4ils.b 2.5 2.7 2.8 2.7 2.8 1.4 2.4 3.2 1.1 - -
-
[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
1bd0.a
1epv.b
1ftx.a
1l6f.a
1l6g.a
1sft.a
1xqk.a
1xql.a
2sfp.a
3uw6.b
4ils.a
4ils.b
[1] 1bd0.a
0
.05 .02 .02 .03 .05 .03 .01 .04 .14 .13 .17
[1] 1epv.b .05
0
.04 .03 .03 .02 .03 .04 .01 .18 .17 .21
[1] 1ftx.a .02 .04
0
.03 .03 .04 .03 .02 .03 .15 .13 .18
[1] 1l6f.a .02 .03 .03
0
0 .03 0 .02 .02 .16 .14 .18
[1] 1l6g.a .03 .03 .03 0
0
.03 0 .01 .02 .17 .14 .19
[1] 1sft.a .05 .02 .04 .03 .03
0
.03 .04 .01 .19 .17 .21
[1] 1xqk.a .03 .03 .03 0 0 .03
0
.01 .02 .17 .14 .19
[1] 1xql.a .01 .04 .02 .02 .01 .04 .01
0
.03 .15 .13 .18
[1] 2sfp.a .04 .01 .03 .02 .02 .01 .02 .03
0
.18 .16 .20
[1] 3uw6.b .14 .18 .15 .16 .17 .19 .17 .15 .18
0
.12 .16
[1] 4ils.a .13 .17 .13 .14 .14 .17 .14 .13 .16 .12
0
.09
[1] 4ils.b .17 .21 .18 .18 .19 .21 .19 .18 .20 .16 .09
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.5 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
1bd0.a
1epv.b
1ftx.a
1l6f.a
1l6g.a
1sft.a
1xqk.a
1xql.a
2sfp.a
3uw6.b
4ils.a
4ils.b
[1] 1bd0.a
0
0.3 0.1 0.1 0.1 0.2 0.2 0.2 0.2 2.0 1.5 1.3
[1] 1epv.b 0.3
0
0.3 0.2 0.2 0.2 0.3 0.2 0.2 1.9 1.4 1.2
[1] 1ftx.a 0.1 0.3
0
0.1 0.1 0.2 0.2 0.1 0.2 1.9 1.5 1.3
[1] 1l6f.a 0.1 0.2 0.1
0
0.1 0.2 0.2 0.1 0.1 1.9 1.5 1.3
[1] 1l6g.a 0.1 0.2 0.1 0.1
0
0.2 0.2 0.1 0.1 1.9 1.5 1.3
[1] 1sft.a 0.2 0.2 0.2 0.2 0.2
0
0.2 0.2 0.2 1.9 1.4 1.3
[1] 1xqk.a 0.2 0.3 0.2 0.2 0.2 0.2
0
0.1 0.2 1.9 1.5 1.3
[1] 1xql.a 0.2 0.2 0.1 0.1 0.1 0.2 0.1
0
0.1 2.0 1.5 1.3
[1] 2sfp.a 0.2 0.2 0.2 0.1 0.1 0.2 0.2 0.1
0
1.9 1.4 1.3
[1] 3uw6.b 2.0 1.9 1.9 1.9 1.9 1.9 1.9 2.0 1.9
0
1.3 1.1
[1] 4ils.a 1.5 1.4 1.5 1.5 1.5 1.4 1.5 1.5 1.4 1.3
0
0.8
[1] 4ils.b 1.3 1.2 1.3 1.3 1.3 1.3 1.3 1.3 1.3 1.1 0.8
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.2 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
1bd0.a
1epv.b
1ftx.a
1l6f.a
1l6g.a
1sft.a
1xqk.a
1xql.a
2sfp.a
3uw6.b
4ils.a
4ils.b
[1] 1bd0.a
0
0.3 0.3 0.4 0.5 0.4 0.4 0.5 0.3 2.1 2.2 1.8
[1] 1epv.b 0.3
0
0.4 0.4 0.5 0.4 0.5 0.5 0.3 2.1 2.1 1.7
[1] 1ftx.a 0.3 0.4
0
0.5 0.5 0.2 0.5 0.4 0.4 2.1 2.1 1.8
[1] 1l6f.a 0.4 0.4 0.5
0
0.3 0.5 0.3 0.3 0.5 2.1 2.1 1.8
[1] 1l6g.a 0.5 0.5 0.5 0.3
0
0.5 0.3 0.4 0.5 2.1 2.1 1.8
[1] 1sft.a 0.4 0.4 0.2 0.5 0.5
0
0.5 0.5 0.4 2.1 2.1 1.8
[1] 1xqk.a 0.4 0.5 0.5 0.3 0.3 0.5
0
0.3 0.5 2.1 2.0 1.8
[1] 1xql.a 0.5 0.5 0.4 0.3 0.4 0.5 0.3
0
0.5 2.1 2.0 1.8
[1] 2sfp.a 0.3 0.3 0.4 0.5 0.5 0.4 0.5 0.5
0
2.1 2.1 1.8
[1] 3uw6.b 2.1 2.1 2.1 2.1 2.1 2.1 2.1 2.1 2.1
0
1.5 1.7
[1] 4ils.a 2.2 2.1 2.1 2.1 2.1 2.1 2.0 2.0 2.1 1.5
0
1.5
[1] 4ils.b 1.8 1.7 1.8 1.8 1.8 1.8 1.8 1.8 1.8 1.7 1.5
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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