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DACC_BACSU_30_491

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

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (DACC_BACSU):R: Substrate binding (330)
R: Substrate binding (442:445)
80, 81, 84, 171, 174, 179, 377:379, 381
80, 81, 84, 171, 174, 179, 330, 377:379, 381, 442:445
Cofactors (cF):dal

Full PDB list

1w5d, 2j9p

Pocket contact map

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PDB.ch
   
ligand
A1 cF
A
8
0
S
8
1
K
8
4
D
1
7
4
Y
1
7
9
N
3
3
0
I
3
7
9
H
3
8
1
G
4
4
2
S
4
4
3
L
4
4
4
S
4
4
5
[1]1w5d.a none . . . . . . . . . . . .
[1]2j9p.b rez16 . * . . . . . . . . . . dal

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 cF
A
8
0
S
8
1
K
8
4
P
1
7
1
D
1
7
4
Y
1
7
9
N
3
3
0
S
3
7
7
G
3
7
8
I
3
7
9
H
3
8
1
G
4
4
2
S
4
4
3
L
4
4
4
S
4
4
5
[1]1w5d.a . . . . . . . . . . . . . . .
[1]2j9p.b . * . . . . . . . . . . . . . dal

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
1w5d.a is apo
2j9p.b:rez
[1] 1w5d.a
-
0.6
[1] 2j9p.b -
0.9
[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
1w5d.a
2j9p.b
[1] 1w5d.a
0
.05
[1] 2j9p.b .05
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.2 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
1w5d.a
2j9p.b
[1] 1w5d.a
0
0.3
[1] 2j9p.b 0.3
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
1w5d.a
2j9p.b
[1] 1w5d.a
0
0.4
[1] 2j9p.b 0.4
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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