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BIODA_ARATH_23_833

Bifunctional dethiobiotin synthetase/7,8-diamino-pelargonic acid aminotransferase, mitochondrial

Composition of the binding site

Protein chains homodimer [domain annotation]
A1 (BIODA_ARATH):R: Dethiobiotin synthetase (46, 80, 81, 163:166, 213, 217, 218)46, 80, 81, 163:166, 213, 217, 218
A2 (BIODA_ARATH):R: Dethiobiotin synthetase (244:248)244:248

Full PDB list

4a0f, 4a0g, 4a0h, 4a0r (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 A2
T
4
6
Q
8
0
T
8
1
A
1
6
3
I
1
6
4
S
1
6
5
P
1
6
6
G
2
1
3
S
2
1
7
L
2
4
4
G
2
4
5
G
2
4
6
I
2
4
7
S
2
4
8
[1]4a0g.a none . . . . . . . . . . . . . .
[1]4a0h.a kap13 . . . . . . . . . . . . . .
[1]4a0r.a dtb15 . . . . . . . . . . . . . .

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
4
6
Q
8
0
T
8
1
A
1
6
3
I
1
6
4
S
1
6
5
P
1
6
6
G
2
1
3
S
2
1
7
P
2
1
8
L
2
4
4
G
2
4
5
G
2
4
6
I
2
4
7
S
2
4
8
[1]4a0g.a . . . . . . . . . . . . . . .
[1]4a0h.a . . . . . . . . . . . . . . .
[1]4a0r.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
4a0g.a is apo
4a0h.a:kap
4a0r.a:dtb
[1] 4a0g.a
-
0 0
[1] 4a0h.a -
0
0.1
[1] 4a0r.a - 0.2
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
4a0g.a
4a0h.a
4a0r.a
[1] 4a0g.a
0
.01 .01
[1] 4a0h.a .01
0
.02
[1] 4a0r.a .01 .02
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.4 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
4a0g.a
4a0h.a
4a0r.a
[1] 4a0g.a
0
0.3 0.5
[1] 4a0h.a 0.3
0
0.4
[1] 4a0r.a 0.5 0.4
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

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
4a0g.a
4a0h.a
4a0r.a
[1] 4a0g.a
0
0.4 0.6
[1] 4a0h.a 0.4
0
0.5
[1] 4a0r.a 0.6 0.5
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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