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BTRN_BACCI_2_250

S-adenosyl-L-methionine-dependent 2-deoxy-scyllo-inosamine dehydrogenase [Radical SAM superfamily]

Composition of the binding site

Protein chains monomer
A1 (BTRN_BACCI):22, 60:64, 90:92, 115, 117, 147:150, 15222, 60:64, 90:92, 115, 117, 147:150, 152
Cofactors (cF):sf4

Full PDB list

4m7s, 4m7t

Pocket contact map

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PDB.ch
   
ligand
A1 cF
Y
2
2
H
6
0
F
6
1
Y
6
2
G
6
3
Y
9
0
T
9
1
N
9
2
T
1
1
5
H
1
1
7
L
1
4
7
V
1
4
8
L
1
4
9
S
1
5
0
R
1
5
2
[1]4m7s.a none . . . . . . . . . . - - - - - sf4
[1]4m7t.a sam27 . . . . . . . . . . . . . . . sf4

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 cF
Y
2
2
H
6
0
F
6
1
Y
6
2
G
6
3
E
6
4
Y
9
0
T
9
1
N
9
2
T
1
1
5
H
1
1
7
L
1
4
7
V
1
4
8
L
1
4
9
S
1
5
0
R
1
5
2
[1]4m7s.a . . . . . . . . . . . - - - - - sf4
[1]4m7t.a . . . . . . . . . . . . . . . . sf4

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
4m7s.a is apo
4m7t.a:sam
[1] 4m7s.a
-
0
[1] 4m7t.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
4m7s.a
4m7t.a
[1] 4m7s.a
0
0
[1] 4m7t.a 0
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
4m7s.a
4m7t.a
[1] 4m7s.a
0
0.8
[1] 4m7t.a 0.8
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

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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
4m7s.a
4m7t.a
[1] 4m7s.a
0
0.9
[1] 4m7t.a 0.9
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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