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BIOD_HELPY_1_218

ATP-dependent dethiobiotin synthetase BioD [Dethiobiotin synthetase family]

Composition of the binding site

Protein chains homodimer
A1 (BIOD_HELPY):9, 39, 79, 80, 119, 1239, 39, 79, 80, 119, 123
A2 (BIOD_HELPY):150:154150:154
Cofactors (cF):gdp/gtp
Metals (Me):Mg

Full PDB list

2qmo, 3mle, 3qxc, 3qxh, 3qxj, 3qxs, 3qxx, 3qy0 (redundant Pocketome entry)

Pocket contact map

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PDB.ch
   
ligand
A1 A2 cF Me
T
9
T
3
9
S
7
9
A
8
0
V
1
2
3
L
1
5
0
G
1
5
1
L
1
5
2
I
1
5
3
N
1
5
4
[1]3qxj.a none . . . . . . . . . . gtp Mg
[1]3qxx.a 8ac11 . . . . . . . . . . gdp Mg

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 cF Me
T
9
T
3
9
S
7
9
A
8
0
G
1
1
9
V
1
2
3
L
1
5
0
G
1
5
1
L
1
5
2
I
1
5
3
N
1
5
4
[1]3qxj.a . . . . . . . . . . . gtp Mg
[1]3qxx.a . . . . . . . . . . . gdp Mg

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
3qxj.a is apo
3qxx.a:8ac
[1] 3qxj.a
-
0
[1] 3qxx.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
3qxj.a
3qxx.a
[1] 3qxj.a
0
0
[1] 3qxx.a 0
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
3qxj.a
3qxx.a
[1] 3qxj.a
0
0.7
[1] 3qxx.a 0.7
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.3 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
3qxj.a
3qxx.a
[1] 3qxj.a
0
0.6
[1] 3qxx.a 0.6
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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