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DACB_ECOLI_20_477

D-alanyl-D-alanine carboxypeptidase DacB [Peptidase S13 family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (DACB_ECOLI):R: Absent in class-A beta-lactamases (155, 160)
61, 62, 65, 305, 306, 308, 358, 359, 361, 398, 402, 417:422, 459
61, 62, 65, 155, 160, 305, 306, 308, 358, 359, 361, 398, 402, 417:422, 459

Full PDB list

2ex2, 2ex6, 2ex8, 2ex9, 2exa, 2exb

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
A
6
1
S
6
2
F
1
6
0
S
3
0
6
N
3
0
8
G
3
5
8
L
3
5
9
R
3
6
1
S
3
9
8
T
4
1
8
G
4
1
9
S
4
2
0
L
4
2
1
Q
4
2
2
[1]2ex2.a none . . . . . . . . . . . . . .
[1]2ex6.a aic24 . * . . . . . . . . . . . .
[1]2ex8.a pnm23 . * . . . . . . . . . . . .
[1]2ex9.a pnv24 . * . . . . . . . . . . . .
[1]2exa.a fpm19 . * . . . . . . . . . . . .
[1]2exb.a fxm38 . * . . . . . . . . . . . .

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
A
6
1
S
6
2
K
6
5
D
1
5
5
F
1
6
0
K
3
0
5
S
3
0
6
N
3
0
8
G
3
5
8
L
3
5
9
R
3
6
1
S
3
9
8
R
4
0
2
K
4
1
7
T
4
1
8
G
4
1
9
S
4
2
0
L
4
2
1
Q
4
2
2
R
4
5
9
[1]2ex2.a . * . . . . . . . . . . . . . . . * . .
[1]2ex6.a . * . . . . . . . . . . . . . . . . . .
[1]2ex8.a . * . . . . . . . . . . . . . . . * . .
[1]2ex9.a . * . . . . . . . . . . . . . . . * . -
[1]2exa.a . * . . . . . . . . . . . . . . . . . .
[1]2exb.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
2ex2.a is apo
2ex6.a:aic
2ex8.a:pnm
2ex9.a:pnv
2exa.a:fpm
2exb.a:fxm
[1] 2ex2.a
-
0.6 0.7 0.7 0.6 2.9
[1] 2ex6.a -
0.8
1.3 0.9 0.9 0.9
[1] 2ex8.a - 0.9
0.7
0.9 0.9 2.5
[1] 2ex9.a - 0.8 1.3
0.8
0.8 2.1
[1] 2exa.a - 0.6 0.8 0.6
0.8
0.9
[1] 2exb.a - 0.6 0.8 0.6 0.7
0.6
[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
2ex2.a
2ex6.a
2ex8.a
2ex9.a
2exa.a
2exb.a
[1] 2ex2.a
0
.15 .05 .07 .12 .11
[1] 2ex6.a .15
0
.12 .09 .04 .05
[1] 2ex8.a .05 .12
0
.05 .11 .12
[1] 2ex9.a .07 .09 .05
0
.09 .11
[1] 2exa.a .12 .04 .11 .09
0
.02
[1] 2exb.a .11 .05 .12 .11 .02
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.2 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
2ex2.a
2ex6.a
2ex8.a
2ex9.a
2exa.a
2exb.a
[1] 2ex2.a
0
1.0 0.3 0.3 1.0 1.2
[1] 2ex6.a 1.0
0
0.9 0.6 0.4 0.5
[1] 2ex8.a 0.3 0.9
0
0.2 1.1 1.2
[1] 2ex9.a 0.3 0.6 0.2
0
0.6 0.8
[1] 2exa.a 1.0 0.4 1.1 0.6
0
0.4
[1] 2exb.a 1.2 0.5 1.2 0.8 0.4
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.5 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
2ex2.a
2ex6.a
2ex8.a
2ex9.a
2exa.a
2exb.a
[1] 2ex2.a
0
1.7 0.8 0.9 1.4 1.6
[1] 2ex6.a 1.7
0
1.8 1.2 1.6 1.6
[1] 2ex8.a 0.8 1.8
0
0.6 1.3 1.5
[1] 2ex9.a 0.9 1.2 0.6
0
0.9 1.2
[1] 2exa.a 1.4 1.6 1.3 0.9
0
0.9
[1] 2exb.a 1.6 1.6 1.5 1.2 0.9
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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