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BIOD_MYCTU_1_226

ATP-dependent dethiobiotin synthetase BioD [Dethiobiotin synthetase family]

Composition of the binding site

Protein chains homodimer [domain annotation]
A1 (BIOD_MYCTU):R: Substrate binding (37, 40, 41)
11, 42, 45, 47, 71:74, 110, 111, 115
11, 37, 40:42, 45, 47, 71:74, 110, 111, 115
A2 (BIOD_MYCTU):R: Substrate binding (144:147)
143, 182
143:147, 182

Full PDB list

3fgn, 3fmf, 3fmi, 3fpa, 4wop (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 A2
T
1
1
K
3
7
Q
4
0
T
4
1
R
4
5
D
4
7
P
7
1
M
7
2
A
7
3
A
1
1
0
G
1
1
1
V
1
1
5
L
1
4
3
G
1
4
4
T
1
4
5
L
1
4
6
N
1
4
7
[1]3fmf.b dsd16 . . . . . . . . . . . . . . . . .
[1]3fmi.a kap13 . . . . . . . . . . . . . . . . .
[1]3fpa.a dtb15 . . . . . . . . . . . . . . . . .
[1]4wop.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

[download in TSV format]
   
PDB.ch
A1 A2
T
1
1
K
3
7
Q
4
0
T
4
1
G
4
2
R
4
5
D
4
7
P
7
1
M
7
2
A
7
3
P
7
4
A
1
1
0
G
1
1
1
V
1
1
5
L
1
4
3
G
1
4
4
T
1
4
5
L
1
4
6
N
1
4
7
N
1
8
2
[1]3fmf.b . . . . . . . . . . . . . . . . . . . .
[1]3fmi.a . . . . . . . . . . . . . . . . . . . .
[1]3fpa.a . . . . . . . . . . . . . . . . . . . .
[1]4wop.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
3fmf.b:dsd
3fmi.a:kap
3fpa.a:dtb
4wop.b is apo
[1] 3fmf.b
0
0 0.3 -
[1] 3fmi.a 0
0
0.1 -
[1] 3fpa.a 0 0.1
0.1
-
[1] 4wop.b 0.1 0.1 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
3fmf.b
3fmi.a
3fpa.a
4wop.b
[1] 3fmf.b
0
.01 .02 .02
[1] 3fmi.a .01
0
.01 .01
[1] 3fpa.a .02 .01
0
.01
[1] 4wop.b .02 .01 .01
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.7 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
3fmf.b
3fmi.a
3fpa.a
4wop.b
[1] 3fmf.b
0
0.4 0.5 0.6
[1] 3fmi.a 0.4
0
0.3 0.5
[1] 3fpa.a 0.5 0.3
0
0.5
[1] 4wop.b 0.6 0.5 0.5
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

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
3fmf.b
3fmi.a
3fpa.a
4wop.b
[1] 3fmf.b
0
0.8 0.8 0.8
[1] 3fmi.a 0.8
0
0.5 0.7
[1] 3fpa.a 0.8 0.5
0
0.8
[1] 4wop.b 0.8 0.7 0.8
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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