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ARNB_SALTY_1_385

UDP-4-amino-4-deoxy-L-arabinose--oxoglutarate aminotransferase [DegT/DnrJ/EryC1 family. ArnB subfamily]

Composition of the binding site

Protein chains monomer
A1 (ARNB_SALTY):12:16, 62:64, 88, 89, 91, 134, 160, 162, 163, 183, 185:188, 297, 329, 33012:16, 62:64, 88, 89, 91, 134, 160, 162, 163, 183, 185:188, 297, 329, 330

Full PDB list

1mdo, 1mdx, 1mdz, 4oca

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
P
1
2
F
1
3
S
1
4
R
1
5
P
1
6
S
6
2
A
6
3
T
6
4
T
8
8
W
8
9
S
9
1
V
1
3
4
D
1
6
0
A
1
6
2
H
1
6
3
S
1
8
3
H
1
8
5
A
1
8
6
I
1
8
7
K
1
8
8
H
3
2
9
F
3
3
0
[1]1mdo.a pmp16 . . . . . . . . . . . . . . . . . . . . . .
[1]1mdx.a plp15 . . . . . . . . . . . . . . . . . . . * . .
[1]1mdz.a dcs,plp37 . . . . . . . . . . . . . . . . . . . * . .
[1]4oca.a 2qr49 . . . . . . . . . . . . . . . . . . . A . .

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
P
1
2
F
1
3
S
1
4
R
1
5
P
1
6
S
6
2
A
6
3
T
6
4
T
8
8
W
8
9
S
9
1
V
1
3
4
D
1
6
0
A
1
6
2
H
1
6
3
S
1
8
3
H
1
8
5
A
1
8
6
I
1
8
7
K
1
8
8
H
2
9
7
H
3
2
9
F
3
3
0
[1]1mdo.a . . . . . . . . . . . . . . . . . . . . . . .
[1]1mdx.a . . . . . . . . . . . . . . . . . . * * . . .
[1]1mdz.a . . . . . . . . . . . . . . . . . . . * . . .
[1]4oca.a . . . . . . . . . . . . . . . . . . . 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
1mdo.a:pmp
1mdx.a:plp
1mdz.a:dcs,plp
4oca.a:2qr
[1] 1mdo.a
0.2
0.3 1.1 0.1
[1] 1mdx.a 0.5
0.6
1.4 0.3
[1] 1mdz.a 0.7 0.9
1.0
0.4
[1] 4oca.a 0.1 0.1 0.6
0.2
[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
1mdo.a
1mdx.a
1mdz.a
4oca.a
[1] 1mdo.a
0
.04 .05 .03
[1] 1mdx.a .04
0
.03 .07
[1] 1mdz.a .05 .03
0
.07
[1] 4oca.a .03 .07 .07
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.3 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
1mdo.a
1mdx.a
1mdz.a
4oca.a
[1] 1mdo.a
0
0.1 0.2 0.2
[1] 1mdx.a 0.1
0
0.1 0.2
[1] 1mdz.a 0.2 0.1
0
0.2
[1] 4oca.a 0.2 0.2 0.2
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
1mdo.a
1mdx.a
1mdz.a
4oca.a
[1] 1mdo.a
0
0.2 0.4 0.5
[1] 1mdx.a 0.2
0
0.2 0.5
[1] 1mdz.a 0.4 0.2
0
0.5
[1] 4oca.a 0.5 0.5 0.5
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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