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DOIS_BACCI_1_368

2-deoxy-scyllo-inosose synthase [Sugar phosphate cyclases superfamily. DOI synthase family]

Composition of the binding site

Protein chains homodimer
A1 (DOIS_BACCI):135, 141, 151, 183, 186, 225, 235, 242, 243, 246, 250, 262, 322135, 141, 151, 183, 186, 225, 235, 242, 243, 246, 250, 262, 322
A2 (DOIS_BACCI):119119
Cofactors (cF):nad
Metals (Me):Co

Full PDB list

2d2x, 2gru

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 A2 cF Me
D
1
3
5
K
1
4
1
N
1
5
1
E
1
8
3
K
1
8
6
K
2
2
5
E
2
3
5
F
2
4
2
E
2
4
3
H
2
4
6
H
2
5
0
H
2
6
2
R
1
1
9
[1]2d2x.b none . . . . . . . . . . . . . Co
[1]2gru.a exo11 . . . . . . . . . . . . . nad Co
[1]2gru.b cak16 . . . . . . . . . . . . . nad Co

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 cF Me
D
1
3
5
K
1
4
1
N
1
5
1
E
1
8
3
K
1
8
6
K
2
2
5
E
2
3
5
F
2
4
2
E
2
4
3
H
2
4
6
H
2
5
0
H
2
6
2
K
3
2
2
R
1
1
9
[1]2d2x.b . . . . . . . . . . . . - . Co
[1]2gru.a . . . . . . . . . . . . . . nad Co
[1]2gru.b . . . . . . . . . . . . - . nad Co

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
2d2x.b is apo
2gru.a:exo
2gru.b:cak
[1] 2d2x.b
-
0 0
[1] 2gru.a -
0
0
[1] 2gru.b - 0.1
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
2d2x.b
2gru.a
2gru.b
[1] 2d2x.b
0
0 .01
[1] 2gru.a 0
0
.01
[1] 2gru.b .01 .01
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.5 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
2d2x.b
2gru.a
2gru.b
[1] 2d2x.b
0
0.4 0.3
[1] 2gru.a 0.4
0
0.4
[1] 2gru.b 0.3 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
2d2x.b
2gru.a
2gru.b
[1] 2d2x.b
0
0.5 0.9
[1] 2gru.a 0.5
0
0.9
[1] 2gru.b 0.9 0.9
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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