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NAGA_ECOLI_1_382

N-acetylglucosamine-6-phosphate deacetylase [Metallo-dependent hydrolases superfamily. NagA family]

Composition of the binding site

Protein chains homodimer [domain annotation]
A1 (NAGA_ECOLI):R: Substrate binding (219, 220)
R: Substrate binding (251)
61, 131, 141, 195, 216, 273, 287, 305
61, 131, 141:143, 195, 216, 219, 220, 251, 273, 287, 305, 306, 308
A2 (NAGA_ECOLI):227227
Metals (Me):Zn

Full PDB list

1ymy, 1yrr, 2p50, 2p53 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 A2 Me
N
6
1
E
1
3
1
G
1
4
1
T
1
4
2
H
1
4
3
H
1
9
5
H
2
1
6
N
2
1
9
A
2
2
0
H
2
5
1
D
2
7
3
F
2
8
7
T
3
0
5
L
3
0
6
G
3
0
8
R
2
2
7
[1]2p50.a none . . . . . . . . . . . . . . . . Zn
[1]2p53.a nng20 . . . . . . . . . . N . . . . . 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

[download in TSV format]
   
PDB.ch
A1 A2 Me
N
6
1
E
1
3
1
G
1
4
1
T
1
4
2
H
1
4
3
H
1
9
5
H
2
1
6
N
2
1
9
A
2
2
0
H
2
5
1
D
2
7
3
F
2
8
7
T
3
0
5
L
3
0
6
G
3
0
8
R
2
2
7
[1]2p50.a . . . . . . . . . . . . . . . . Zn
[1]2p53.a . . . . . . . . . . N . . . . . 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
2p50.a is apo
2p53.a:nng
[1] 2p50.a
-
0.1
[1] 2p53.a -
0
[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
2p50.a
2p53.a
[1] 2p50.a
0
.01
[1] 2p53.a .01
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
2p50.a
2p53.a
[1] 2p50.a
0
1.0
[1] 2p53.a 1.0
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
2p50.a
2p53.a
[1] 2p50.a
0
1.1
[1] 2p53.a 1.1
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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