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ALR1_ECOLI_2_359

Alanine racemase, biosynthetic [Alanine racemase family]

Composition of the binding site

Protein chains homodimer
A1 (ALR1_ECOLI):32, 34, 38, 78, 122, 129, 159, 193, 194, 209, 211, 212, 34332, 34, 38, 78, 122, 129, 159, 193, 194, 209, 211, 212, 343
A2 (ALR1_ECOLI):255, 274, 302:304255, 274, 302:304

Full PDB list

2rjg, 2rjh, 3b8t, 3b8u, 3b8v, 3b8w, 4wr3, 4xbj (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 A2
V
3
2
K
3
4
Y
3
8
L
7
8
R
1
2
9
H
1
5
9
A
1
9
3
S
1
9
4
R
2
0
9
G
2
1
1
I
2
1
2
Y
3
4
3
Y
2
5
5
Y
2
7
4
A
3
0
2
M
3
0
3
[1]2rjh.a dcs22 . . . . . . . . . . . . . . . .
[1]3b8v.a plp15 . * . . . . . . . . . . . . . .
[1]4wr3.a plp15 . * . . . . . . . . . . . F . .
[1]4xbj.c in522 . . . . . . . . . . . . . F . .
[1]4xbj.d none . . . . . . . . . . . . . F . .

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
2
K
3
4
Y
3
8
L
7
8
K
1
2
2
R
1
2
9
H
1
5
9
A
1
9
3
S
1
9
4
R
2
0
9
G
2
1
1
I
2
1
2
Y
3
4
3
Y
2
5
5
Y
2
7
4
A
3
0
2
M
3
0
3
D
3
0
4
[1]2rjh.a . . . . * . . . . . . . . . . . . .
[1]3b8v.a . * . . * . . . . . . . . . . . . .
[1]4wr3.a . * . . . . . . . . . . . . F . . .
[1]4xbj.c . * . . . . . . . . . . . . F . . .
[1]4xbj.d . . . . . . . . . . . . . . F . . .

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
2rjh.a:dcs
3b8v.a:plp
4wr3.a:plp
4xbj.c:in5
4xbj.d is apo
[1] 2rjh.a
0.1
0.4 0.1 0.3 -
[1] 3b8v.a 0.3
0.8
0.6 0.5 -
[1] 4wr3.a 0.3 0.8
0.7
0.4 -
[1] 4xbj.c 0.1 0.6 0.5
0.2
-
[1] 4xbj.d 0.3 0.4 0.4 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
2rjh.a
3b8v.a
4wr3.a
4xbj.c
4xbj.d
[1] 2rjh.a
0
.03 .04 .03 .01
[1] 3b8v.a .03
0
.03 .03 .04
[1] 4wr3.a .04 .03
0
.03 .03
[1] 4xbj.c .03 .03 .03
0
.03
[1] 4xbj.d .01 .04 .03 .03
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.7 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
2rjh.a
3b8v.a
4wr3.a
4xbj.c
4xbj.d
[1] 2rjh.a
0
0.2 0.2 0.2 0.3
[1] 3b8v.a 0.2
0
0.1 0.2 0.3
[1] 4wr3.a 0.2 0.1
0
0.2 0.2
[1] 4xbj.c 0.2 0.2 0.2
0
0.2
[1] 4xbj.d 0.3 0.3 0.2 0.2
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
2rjh.a
3b8v.a
4wr3.a
4xbj.c
4xbj.d
[1] 2rjh.a
0
0.7 0.7 1.0 0.8
[1] 3b8v.a 0.7
0
0.7 0.7 0.6
[1] 4wr3.a 0.7 0.7
0
0.7 0.6
[1] 4xbj.c 1.0 0.7 0.7
0
0.5
[1] 4xbj.d 0.8 0.6 0.6 0.5
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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