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DACA_ECOLI_30_392

D-alanyl-D-alanine carboxypeptidase DacA [Peptidase S11 family]

Composition of the binding site

Protein chains monomer
A1 (DACA_ECOLI):72, 73, 76, 114:116, 138, 139, 141, 180:182, 227, 243:247, 274, 27772, 73, 76, 114:116, 138, 139, 141, 180:182, 227, 243:247, 274, 277

Full PDB list

1hd8, 1nj4, 1nzo, 1nzu, 1sdn, 1z6f, 3beb, 3bec, 3mzd, 3mze, 3mzf, 4drt, 5j8x (redundant Pocketome entry)

Pocket contact map

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PDB.ch
   
ligand
A1
A
7
2
S
7
3
K
7
6
G
1
1
4
S
1
1
5
S
1
1
6
S
1
3
9
N
1
4
1
G
1
8
1
L
1
8
2
R
2
2
7
T
2
4
3
G
2
4
4
H
2
4
5
T
2
4
6
D
2
4
7
F
2
7
4
R
2
7
7
[1]1nzo.a none . . . . . . . . . . . . . . . . . .
[1]1z6f.a bo917 . * . . . . . . . . . . . . . . . .
[1]3beb.a hj318 . * . . . . . . . . . . . . . . . .
[1]3bec.a hj213 . * . . . . . . . . . . . . . . . .
[1]3mzd.a cxv23 . * . . . . . . . . . . . . . . . .
[1]3mze.a cfx17 . * . . . . . . . . . . . . . . . .
[1]3mzf.a im218 . * . . . . . . . . . . . . . . . .
[1]4drt.a none . L H . A . D A . G . . . . . . . .
[1]5j8x.a ok325 . * . - - - . . . . . . . . . . . .

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
7
2
S
7
3
K
7
6
G
1
1
4
S
1
1
5
S
1
1
6
Q
1
3
8
S
1
3
9
N
1
4
1
H
1
8
0
G
1
8
1
L
1
8
2
R
2
2
7
T
2
4
3
G
2
4
4
H
2
4
5
T
2
4
6
D
2
4
7
F
2
7
4
R
2
7
7
[1]1nzo.a . * . . . . . . . . . * . . . . . . . .
[1]1z6f.a . * . . . . . . . . . * . . . . . . . .
[1]3beb.a . * . . . . . . . . . * . . . . . . . .
[1]3bec.a . * . . . . . . . . . * . . . . . . . .
[1]3mzd.a . * . . . . . . . . . . . . . . . . . .
[1]3mze.a . * . . . . . . . . . * . . . . . . . .
[1]3mzf.a . * . . . . . . . . . * . . . . . . . .
[1]4drt.a . L H . A . . D A S . G * . . . . . . .
[1]5j8x.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
1nzo.a is apo
1z6f.a:bo9
3beb.a:hj3
3bec.a:hj2
3mzd.a:cxv
3mze.a:cfx
3mzf.a:im2
4drt.a is apo
5j8x.a:ok3
[1] 1nzo.a
-
0.8 0.4 0.7 1.3 0.6 0.8 - 0.6
[1] 1z6f.a -
0.4
0.4 0.3 1.7 0.8 0.5 - 1.0
[1] 3beb.a - 1.1
0.6
0.9 1.4 1.0 1.0 - 0.7
[1] 3bec.a - 1.1 0.5
0.7
1.5 0.6 0.7 - 0.6
[1] 3mzd.a - 1.0 0.7 0.9
0.7
1.3 1.0 - 0.9
[1] 3mze.a - 0.9 0.9 1.6 2.3
0.7
0.8 - 0.8
[1] 3mzf.a - 0.8 0.7 0.7 1.4 0.9
0.8
- 0.9
[1] 4drt.a - 2.8 1.6 2.0 2.0 2.6 2.5
-
2.8
[1] 5j8x.a - 1.4 1.6 1.6 2.7 1.1 1.1 -
0.7
[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
1nzo.a
1z6f.a
3beb.a
3bec.a
3mzd.a
3mze.a
3mzf.a
4drt.a
5j8x.a
[1] 1nzo.a
0
.10 .02 .03 .07 .09 .03 .20 .14
[1] 1z6f.a .10
0
.12 .11 .13 .16 .07 .23 .17
[1] 3beb.a .02 .12
0
.03 .08 .09 .06 .19 .13
[1] 3bec.a .03 .11 .03
0
.08 .11 .05 .18 .13
[1] 3mzd.a .07 .13 .08 .08
0
.16 .06 .16 .16
[1] 3mze.a .09 .16 .09 .11 .16
0
.12 .29 .14
[1] 3mzf.a .03 .07 .06 .05 .06 .12
0
.20 .13
[1] 4drt.a .20 .23 .19 .18 .16 .29 .20
0
.27
[1] 5j8x.a .14 .17 .13 .13 .16 .14 .13 .27
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.9 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
1nzo.a
1z6f.a
3beb.a
3bec.a
3mzd.a
3mze.a
3mzf.a
4drt.a
5j8x.a
[1] 1nzo.a
0
1.0 0.5 1.0 0.8 1.0 0.6 5.2 1.4
[1] 1z6f.a 1.0
0
1.1 1.4 0.4 1.3 0.8 5.3 1.0
[1] 3beb.a 0.5 1.1
0
0.9 0.9 1.1 0.6 5.3 1.4
[1] 3bec.a 1.0 1.4 0.9
0
1.3 0.5 1.0 5.3 1.2
[1] 3mzd.a 0.8 0.4 0.9 1.3
0
1.2 0.7 5.3 1.0
[1] 3mze.a 1.0 1.3 1.1 0.5 1.2
0
1.1 5.3 1.0
[1] 3mzf.a 0.6 0.8 0.6 1.0 0.7 1.1
0
5.3 1.3
[1] 4drt.a 5.2 5.3 5.3 5.3 5.3 5.3 5.3
0
2.1
[1] 5j8x.a 1.4 1.0 1.4 1.2 1.0 1.0 1.3 2.1
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 1.0 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
1nzo.a
1z6f.a
3beb.a
3bec.a
3mzd.a
3mze.a
3mzf.a
4drt.a
5j8x.a
[1] 1nzo.a
0
1.1 0.7 1.9 1.2 2.0 0.9 4.8 2.3
[1] 1z6f.a 1.1
0
1.0 2.0 1.0 2.1 0.9 4.8 2.0
[1] 3beb.a 0.7 1.0
0
1.7 1.2 1.9 0.7 4.8 2.1
[1] 3bec.a 1.9 2.0 1.7
0
2.0 1.3 1.8 5.1 1.6
[1] 3mzd.a 1.2 1.0 1.2 2.0
0
2.1 1.1 4.8 2.1
[1] 3mze.a 2.0 2.1 1.9 1.3 2.1
0
2.0 5.1 1.5
[1] 3mzf.a 0.9 0.9 0.7 1.8 1.1 2.0
0
4.8 2.1
[1] 4drt.a 4.8 4.8 4.8 5.1 4.8 5.1 4.8
0
3.0
[1] 5j8x.a 2.3 2.0 2.1 1.6 2.1 1.5 2.1 3.0
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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