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CQSA_VIBCH_1_389

CAI-1 autoinducer synthase [Class-II pyridoxal-phosphate-dependent aminotransferase family]

Composition of the binding site

Protein chains homodimer
A1 (CQSA_VIBCH):30, 32, 47, 107:109, 112, 133, 135, 173, 177, 202, 204, 205, 233, 235, 236, 344:349, 35830, 32, 47, 107:109, 112, 133, 135, 173, 177, 202, 204, 205, 233, 235, 236, 344:349, 358
A2 (CQSA_VIBCH):76, 78, 79, 257, 263:26676, 78, 79, 257, 263:266

Full PDB list

2wk7, 2wk8, 2wk9, 2wka, 3hqt, 3kki (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 A2
H
3
0
V
3
2
N
4
7
S
1
0
7
G
1
0
8
W
1
0
9
N
1
1
2
H
1
3
3
D
1
7
3
S
1
7
7
D
2
0
2
S
2
0
4
H
2
0
5
S
2
3
3
K
2
3
6
V
3
4
4
F
3
4
5
C
3
4
6
P
3
4
8
A
3
4
9
R
3
5
8
S
7
6
F
7
9
F
2
5
7
I
2
6
3
F
2
6
4
S
2
6
5
S
2
6
6
[1]2wk7.a none . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2wk9.b plg20 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2wka.a p8928 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3hqt.a plp16 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3kki.a dtt,mg,plp25 . . . . . . . . . . . . . . . . . . . . . . . . . . . .

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 A2
H
3
0
V
3
2
N
4
7
S
1
0
7
G
1
0
8
W
1
0
9
N
1
1
2
H
1
3
3
S
1
3
5
D
1
7
3
S
1
7
7
D
2
0
2
S
2
0
4
H
2
0
5
S
2
3
3
A
2
3
5
K
2
3
6
V
3
4
4
F
3
4
5
C
3
4
6
R
3
4
7
P
3
4
8
A
3
4
9
R
3
5
8
S
7
6
S
7
8
F
7
9
F
2
5
7
I
2
6
3
F
2
6
4
S
2
6
5
S
2
6
6
[1]2wk7.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2wk9.b . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2wka.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3hqt.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3kki.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
2wk7.a is apo
2wk9.b:plg
2wka.a:p89
3hqt.a:plp
3kki.a:dtt,mg,plp
[1] 2wk7.a
-
0.1 0.2 0.2 0
[1] 2wk9.b -
0.3
0.3 0.4 0.2
[1] 2wka.a - 0.2
0.2
0.4 0.3
[1] 3hqt.a - 0.7 0.6
0.5
0.2
[1] 3kki.a - 0.2 0.1 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
2wk7.a
2wk9.b
2wka.a
3hqt.a
3kki.a
[1] 2wk7.a
0
.02 .02 .03 .01
[1] 2wk9.b .02
0
.01 .03 .02
[1] 2wka.a .02 .01
0
.02 .02
[1] 3hqt.a .03 .03 .02
0
.02
[1] 3kki.a .01 .02 .02 .02
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
2wk7.a
2wk9.b
2wka.a
3hqt.a
3kki.a
[1] 2wk7.a
0
0.4 0.3 0.4 0.4
[1] 2wk9.b 0.4
0
0.2 0.2 0.2
[1] 2wka.a 0.3 0.2
0
0.3 0.3
[1] 3hqt.a 0.4 0.2 0.3
0
0.2
[1] 3kki.a 0.4 0.2 0.3 0.2
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

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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
2wk7.a
2wk9.b
2wka.a
3hqt.a
3kki.a
[1] 2wk7.a
0
0.5 0.3 0.8 0.8
[1] 2wk9.b 0.5
0
0.4 0.7 0.7
[1] 2wka.a 0.3 0.4
0
0.8 0.7
[1] 3hqt.a 0.8 0.7 0.8
0
0.3
[1] 3kki.a 0.8 0.7 0.7 0.3
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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