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DACB_HAEIN_27_479

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

Composition of the binding site

Protein chains monomer
A1 (DACB_HAEIN):68, 69, 72, 159, 162, 167, 168, 310, 312, 362, 401, 421:42468, 69, 72, 159, 162, 167, 168, 310, 312, 362, 401, 421:424

Full PDB list

3a3d, 3a3e, 3a3f, 3a3i

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
A
6
8
S
6
9
D
1
6
2
F
1
6
7
N
1
6
8
S
3
1
0
N
3
1
2
L
3
6
2
T
4
0
1
T
4
2
1
G
4
2
2
S
4
2
3
L
4
2
4
[1]3a3d.a none . . . . . . . . . . . . .
[1]3a3e.a cmv34 . * - . . . . . . . . . .
[1]3a3f.a fmz30 . * . . . . . . . . . . .
[1]3a3i.a aix24 . * . . . . . . . . . . .

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
8
S
6
9
K
7
2
I
1
5
9
D
1
6
2
F
1
6
7
N
1
6
8
S
3
1
0
N
3
1
2
L
3
6
2
T
4
0
1
T
4
2
1
G
4
2
2
S
4
2
3
L
4
2
4
[1]3a3d.a . * . . * * . . . . . . . . .
[1]3a3e.a . * . - - . . . . . . . . . .
[1]3a3f.a . * . . . . . . . . . . . . .
[1]3a3i.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
3a3d.a is apo
3a3e.a:cmv
3a3f.a:fmz
3a3i.a:aix
[1] 3a3d.a
-
4.4 1.8 0.9
[1] 3a3e.a -
0.7
1.0 1.0
[1] 3a3f.a - 2.3
0.8
0.7
[1] 3a3i.a - 3.8 1.7
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
3a3d.a
3a3e.a
3a3f.a
3a3i.a
[1] 3a3d.a
0
.27 .16 .05
[1] 3a3e.a .27
0
.11 .23
[1] 3a3f.a .16 .11
0
.11
[1] 3a3i.a .05 .23 .11
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.6 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
3a3d.a
3a3e.a
3a3f.a
3a3i.a
[1] 3a3d.a
0
0.5 0.4 0.3
[1] 3a3e.a 0.5
0
0.5 0.4
[1] 3a3f.a 0.4 0.5
0
0.2
[1] 3a3i.a 0.3 0.4 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
3a3d.a
3a3e.a
3a3f.a
3a3i.a
[1] 3a3d.a
0
1.4 0.7 0.4
[1] 3a3e.a 1.4
0
1.3 1.4
[1] 3a3f.a 0.7 1.3
0
0.5
[1] 3a3i.a 0.4 1.4 0.5
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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