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DPDS_MYCTU_13_296

Decaprenyl diphosphate synthase [UPP synthase family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (DPDS_MYCTU):R: Substrate binding (76:80)
R: Substrate binding (124)
75, 83, 84, 89, 93, 96, 100, 118, 119, 127, 135, 138, 139, 191, 271
75:80, 83, 84, 89, 93, 96, 100, 118, 119, 124, 127, 135, 138, 139, 191, 271

Full PDB list

2vg2, 2vg3, 2vg4, 4onc

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
M
7
5
D
7
6
G
7
7
N
7
8
G
7
9
R
8
0
T
8
3
R
8
9
H
9
3
G
9
6
V
1
0
0
A
1
1
9
R
1
2
7
W
2
7
1
[1]2vg2.a dpo9 . . . . . . . . . . . . . .
[1]2vg3.a gpp,mg20 . . . . . . . . . . . . . .
[1]2vg4.c none . . . . . . . . . . . . . .
[1]4onc.a 40b28 . . . . . . . . . . . . . .

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
M
7
5
D
7
6
G
7
7
N
7
8
G
7
9
R
8
0
T
8
3
Q
8
4
R
8
9
H
9
3
G
9
6
V
1
0
0
Y
1
1
8
A
1
1
9
N
1
2
4
R
1
2
7
L
1
3
5
F
1
3
8
N
1
3
9
Y
1
9
1
W
2
7
1
[1]2vg2.a . . . . . . . . * . . . . . . . . . . . .
[1]2vg3.a . . . . . . . . * . . . . . . . . . . . .
[1]2vg4.c . . . . . * . . * . . . . . . . . . . . .
[1]4onc.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
2vg2.a:dpo
2vg3.a:gpp,mg
2vg4.c is apo
4onc.a:40b
[1] 2vg2.a
0.1
0.8 - 2.2
[1] 2vg3.a 0.1
0.1
- 0.8
[1] 2vg4.c 0.5 1.1
-
2.2
[1] 4onc.a 0.8 1.4 -
0.1
[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
2vg2.a
2vg3.a
2vg4.c
4onc.a
[1] 2vg2.a
0
.07 .06 .05
[1] 2vg3.a .07
0
.09 .05
[1] 2vg4.c .06 .09
0
.10
[1] 4onc.a .05 .05 .10
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.8 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
2vg2.a
2vg3.a
2vg4.c
4onc.a
[1] 2vg2.a
0
0.4 0.4 0.5
[1] 2vg3.a 0.4
0
0.5 0.3
[1] 2vg4.c 0.4 0.5
0
0.6
[1] 4onc.a 0.5 0.3 0.6
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

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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
2vg2.a
2vg3.a
2vg4.c
4onc.a
[1] 2vg2.a
0
0.4 0.8 1.0
[1] 2vg3.a 0.4
0
0.8 0.9
[1] 2vg4.c 0.8 0.8
0
1.3
[1] 4onc.a 1.0 0.9 1.3
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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