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AMN_ECOLI_1_484

AMP nucleosidase [AMP nucleosidase family]

Composition of the binding site

Protein chains homodimer
A1 (AMN_ECOLI):205, 280, 305:307, 381, 383, 402:405, 428, 430, 436:438205, 280, 305:307, 381, 383, 402:405, 428, 430, 436:438
A2 (AMN_ECOLI):188, 189, 259188, 189, 259

Full PDB list

1t8r, 1t8s, 1t8w, 1t8y, 2guw (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 A2
N
2
0
5
H
3
0
5
C
3
0
6
G
3
0
7
R
3
8
1
W
3
8
3
I
4
0
2
D
4
0
3
M
4
0
4
E
4
0
5
D
4
2
8
P
4
3
0
K
4
3
6
H
1
8
8
Y
1
8
9
[1]1t8s.b fmp23 . . . . . . . . * . . . . . .
[1]1t8w.a none . . . . . . . . * . . . . . .
[1]2guw.b none . . . . . . . . . . . . . . .

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 A2
N
2
0
5
V
2
8
0
H
3
0
5
C
3
0
6
G
3
0
7
R
3
8
1
W
3
8
3
I
4
0
2
D
4
0
3
M
4
0
4
E
4
0
5
D
4
2
8
P
4
3
0
K
4
3
6
L
4
3
7
P
4
3
8
H
1
8
8
Y
1
8
9
Q
2
5
9
[1]1t8s.b . . . . . . . . . * . . . . - - . . .
[1]1t8w.a . . . . . . . . . * . . . . . . . . .
[1]2guw.b . . . . . . . . . . . . . . . . . . .

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
1t8s.b:fmp
1t8w.a is apo
2guw.b is apo
[1] 1t8s.b
0
- -
[1] 1t8w.a 1.2
-
-
[1] 2guw.b 1.0 -
-
[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
1t8s.b
1t8w.a
2guw.b
[1] 1t8s.b
0
.06 .05
[1] 1t8w.a .06
0
.03
[1] 2guw.b .05 .03
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.4 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
1t8s.b
1t8w.a
2guw.b
[1] 1t8s.b
0
0.9 0.8
[1] 1t8w.a 0.9
0
0.3
[1] 2guw.b 0.8 0.3
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.4 Å)

Pockets (x) vs pockets (y) colored by RMSD of all site residue atoms

zoom: [−] [+]; [view as image]; [download as text]

pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
1t8s.b
1t8w.a
2guw.b
[1] 1t8s.b
0
2.1 1.7
[1] 1t8w.a 2.1
0
1.4
[1] 2guw.b 1.7 1.4
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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