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AMPD_CITFR_1_187

1,6-anhydro-N-acetylmuramyl-L-alanine amidase AmpD [N-acetylmuramoyl-L-alanine amidase 2 family]

Composition of the binding site

Protein chains monomer
A1 (AMPD_CITFR):34, 52, 71:73, 95:98, 107, 109, 116, 154, 161, 16234, 52, 71:73, 95:98, 107, 109, 116, 154, 161, 162
Metals (Me):Zn

Full PDB list

2y28, 2y2b, 2y2c, 2y2d, 2y2e (redundant Pocketome entry)

Pocket contact map

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PDB.ch
   
ligand
A1 Me
H
3
4
F
5
2
R
7
1
V
7
2
S
7
3
W
9
5
H
9
6
A
9
7
G
9
8
R
1
0
7
N
1
0
9
E
1
1
6
H
1
5
4
R
1
6
1
[1]2y2b.a mhi27 . . . . . . . . . . . . . . Zn
[1]2y2d.c none . . . . . . . . . . . . . . Zn

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 Me
H
3
4
F
5
2
R
7
1
V
7
2
S
7
3
W
9
5
H
9
6
A
9
7
G
9
8
R
1
0
7
N
1
0
9
E
1
1
6
H
1
5
4
R
1
6
1
K
1
6
2
[1]2y2b.a . . . . . . . . . . . . . . . Zn
[1]2y2d.c . . * . . . . . . . . . . . . Zn

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
2y2b.a:mhi
2y2d.c is apo
[1] 2y2b.a
0
-
[1] 2y2d.c 1.5
-
[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
2y2b.a
2y2d.c
[1] 2y2b.a
0
.10
[1] 2y2d.c .10
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
2y2b.a
2y2d.c
[1] 2y2b.a
0
0.2
[1] 2y2d.c 0.2
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.1 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
2y2b.a
2y2d.c
[1] 2y2b.a
0
1.2
[1] 2y2d.c 1.2
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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