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BIOD1_ECOLI_2_225

ATP-dependent dethiobiotin synthetase BioD 1 [Dethiobiotin synthetase family]

Composition of the binding site

Protein chains homodimer
A1 (BIOD1_ECOLI):12:18, 38, 41, 42, 55, 80:83, 116, 118, 119, 123, 124, 176, 177, 204:209, 211, 21212:18, 38, 41, 42, 55, 80:83, 116, 118, 119, 123, 124, 176, 177, 204:209, 211, 212
A2 (BIOD1_ECOLI):150:154, 188150:154, 188

Full PDB list

1a82, 1bs1, 1byi, 1dad, 1dae, 1daf, 1dag, 1dah, 1dai, 1dak, 1dam, 1dbs, 1dts (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 A2
T
1
2
E
1
3
V
1
4
G
1
5
K
1
6
T
1
7
V
1
8
K
3
8
A
4
1
S
4
2
D
5
5
P
8
0
T
8
1
S
8
2
E
1
1
6
A
1
1
8
G
1
1
9
T
1
2
3
P
1
2
4
N
1
7
6
D
1
7
7
I
2
0
4
P
2
0
5
W
2
0
6
L
2
0
7
P
2
1
1
E
2
1
2
L
1
5
0
G
1
5
1
C
1
5
2
I
1
5
3
N
1
5
4
Y
1
8
8
[1]1a82.a atp,dnn,mg45 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1bs1.a adp,daa,mg,mg49 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1byi.a none . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1dad.a adp27 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1dae.a ikt16 . . . . . . . . . . . . . . . . . . . . . . . . . - - . . . . . .
[1]1daf.a adp,ca,dsd44 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1dag.a acp,dsd47 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1dah.a acp,dnn,mn45 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1dai.a dsd16 . . . . . . . . . . . . . . . . . . . . . . . . . - - . . . . . .
[1]1dak.a adp,dpu,mg,mg49 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1dam.a adp,dtb,mg,mg44 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

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
2
E
1
3
V
1
4
G
1
5
K
1
6
T
1
7
V
1
8
K
3
8
A
4
1
S
4
2
D
5
5
P
8
0
T
8
1
S
8
2
P
8
3
E
1
1
6
A
1
1
8
G
1
1
9
T
1
2
3
P
1
2
4
N
1
7
6
D
1
7
7
I
2
0
4
P
2
0
5
W
2
0
6
L
2
0
7
A
2
0
8
E
2
0
9
P
2
1
1
E
2
1
2
L
1
5
0
G
1
5
1
C
1
5
2
I
1
5
3
N
1
5
4
Y
1
8
8
[1]1a82.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1bs1.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1byi.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1dad.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1dae.a . . . . . . . . . . . . . . . . . . . . . . . . . . . - - - . . . . . .
[1]1daf.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1dag.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1dah.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1dai.a . . . . . . . . . . . . . . . . . . . . . . . . . . . - - - . . . . . .
[1]1dak.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1dam.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
1a82.a:atp,dnn,mg
1bs1.a:adp,daa,mg
1byi.a is apo
1dad.a:adp
1dae.a:ikt
1daf.a:adp,ca,dsd
1dag.a:acp,dsd
1dah.a:acp,dnn,mn
1dai.a:dsd
1dak.a:adp,dpu,mg
1dam.a:adp,dtb,mg
[1] 1a82.a
0.3
0.3 - 0.1 0.1 0 0.1 0.4 0.1 0.3 0.5
[1] 1bs1.a 0.3
0.3
- 0 0 0 0.1 0.5 0 0.3 0.4
[1] 1byi.a 0.7 0.7
-
0.2 0.2 0.4 0.4 0.6 0.1 0.7 0.6
[1] 1dad.a 0.1 0.1 -
0
0 0.1 0 0.1 0 0.2 0.4
[1] 1dae.a 0.8 0.9 - 0.7
0
0.5 0.5 0.8 0 0.7 1.0
[1] 1daf.a 0.2 0.2 - 0.1 0.1
0.2
0.1 0.1 0 0.3 0.3
[1] 1dag.a 0.3 0.2 - 0 0 0.3
0
0.2 0 0.3 0.5
[1] 1dah.a 0.2 0.1 - 0.1 0 0.2 0
0.3
0 0 0.4
[1] 1dai.a 0.7 0.7 - 0.4 0 0.5 0.3 0.5
0
0.5 0.7
[1] 1dak.a 0.4 0.4 - 0.1 0 0 0.4 0.9 0
0.3
0.6
[1] 1dam.a 0.4 0.3 - 0 0 0 0.4 0.9 0 0.4
0.3
[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
1a82.a
1bs1.a
1byi.a
1dad.a
1dae.a
1daf.a
1dag.a
1dah.a
1dai.a
1dak.a
1dam.a
[1] 1a82.a
0
.01 .03 .02 .03 .01 .03 0 .03 .02 .03
[1] 1bs1.a .01
0
.03 .02 .04 .01 .02 .01 .03 .02 .02
[1] 1byi.a .03 .03
0
.03 .03 .03 .03 .03 .02 .05 .04
[1] 1dad.a .02 .02 .03
0
.03 .03 .03 .02 .02 .04 .03
[1] 1dae.a .03 .04 .03 .03
0
.03 .03 .03 .01 .04 .05
[1] 1daf.a .01 .01 .03 .03 .03
0
.02 .02 .03 .02 .03
[1] 1dag.a .03 .02 .03 .03 .03 .02
0
.02 .03 .03 .03
[1] 1dah.a 0 .01 .03 .02 .03 .02 .02
0
.02 .02 .03
[1] 1dai.a .03 .03 .02 .02 .01 .03 .03 .02
0
.04 .04
[1] 1dak.a .02 .02 .05 .04 .04 .02 .03 .02 .04
0
.01
[1] 1dam.a .03 .02 .04 .03 .05 .03 .03 .03 .04 .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
1a82.a
1bs1.a
1byi.a
1dad.a
1dae.a
1daf.a
1dag.a
1dah.a
1dai.a
1dak.a
1dam.a
[1] 1a82.a
0
0.1 1.9 0.4 0.6 0.3 0.3 0.3 0.6 0.1 0.2
[1] 1bs1.a 0.1
0
1.9 0.4 0.5 0.2 0.3 0.3 0.5 0.1 0.2
[1] 1byi.a 1.9 1.9
0
1.9 0.7 1.9 1.9 1.9 0.6 1.9 1.9
[1] 1dad.a 0.4 0.4 1.9
0
0.5 0.3 0.3 0.3 0.4 0.4 0.4
[1] 1dae.a 0.6 0.5 0.7 0.5
0
0.5 0.4 0.4 0.4 0.5 0.5
[1] 1daf.a 0.3 0.2 1.9 0.3 0.5
0
0.2 0.3 0.5 0.2 0.3
[1] 1dag.a 0.3 0.3 1.9 0.3 0.4 0.2
0
0.1 0.4 0.3 0.3
[1] 1dah.a 0.3 0.3 1.9 0.3 0.4 0.3 0.1
0
0.4 0.3 0.3
[1] 1dai.a 0.6 0.5 0.6 0.4 0.4 0.5 0.4 0.4
0
0.6 0.6
[1] 1dak.a 0.1 0.1 1.9 0.4 0.5 0.2 0.3 0.3 0.6
0
0.2
[1] 1dam.a 0.2 0.2 1.9 0.4 0.5 0.3 0.3 0.3 0.6 0.2
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
1a82.a
1bs1.a
1byi.a
1dad.a
1dae.a
1daf.a
1dag.a
1dah.a
1dai.a
1dak.a
1dam.a
[1] 1a82.a
0
0.3 2.7 0.7 0.9 0.5 0.6 0.5 1.0 0.3 0.5
[1] 1bs1.a 0.3
0
2.7 0.8 0.8 0.5 0.6 0.5 0.9 0.2 0.4
[1] 1byi.a 2.7 2.7
0
2.6 0.8 2.7 2.6 2.6 0.8 2.7 2.6
[1] 1dad.a 0.7 0.8 2.6
0
0.8 0.7 0.7 0.7 0.9 0.8 0.8
[1] 1dae.a 0.9 0.8 0.8 0.8
0
0.9 0.8 0.8 0.4 0.7 0.7
[1] 1daf.a 0.5 0.5 2.7 0.7 0.9
0
0.5 0.5 1.0 0.6 0.7
[1] 1dag.a 0.6 0.6 2.6 0.7 0.8 0.5
0
0.3 0.9 0.6 0.7
[1] 1dah.a 0.5 0.5 2.6 0.7 0.8 0.5 0.3
0
0.9 0.5 0.6
[1] 1dai.a 1.0 0.9 0.8 0.9 0.4 1.0 0.9 0.9
0
0.8 0.8
[1] 1dak.a 0.3 0.2 2.7 0.8 0.7 0.6 0.6 0.5 0.8
0
0.4
[1] 1dam.a 0.5 0.4 2.6 0.8 0.7 0.7 0.7 0.6 0.8 0.4
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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