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CPXJ_SACEN_2_404

6-deoxyerythronolide B hydroxylase [Cytochrome P450 family]

Composition of the binding site

Protein chains monomer
A1 (CPXJ_SACEN):59, 61, 72, 74, 75, 78, 86, 89, 91, 92, 171, 174, 175, 185, 237, 240, 241, 244, 245, 288, 292, 351, 391, 39259, 61, 72, 74, 75, 78, 86, 89, 91, 92, 171, 174, 175, 185, 237, 240, 241, 244, 245, 288, 292, 351, 391, 392
Cofactors (cF):hem
Metals (Me):Fe

Full PDB list

1egy, 1eup, 1jin, 1jio, 1jip, 1oxa, 1z8o, 1z8p, 1z8q (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 cF Me
S
5
9
P
6
1
F
7
2
A
7
4
Y
7
5
F
7
8
F
8
6
N
8
9
G
9
1
T
9
2
S
1
7
1
I
1
7
4
L
1
7
5
R
1
8
5
V
2
3
7
L
2
4
0
A
2
4
1
E
2
4
4
A
2
4
5
P
2
8
8
T
2
9
2
L
3
9
1
L
3
9
2
[1]1egy.a 9ap,9ap30 . . . . . . . . . . . . . . . . . . . . . . . hem Fe
[1]1eup.a asd,asd42 . . . . . . . . . . . . . . . . . . . . . . . hem Fe
[1]1jin.a ktn36 . . . . . . . . . . . . . . . . . . . . . . . hem Fe
[1]1jip.a ktn36 . . . . . . . . . . . . . . . . . . S . . . . hem Fe
[1]1z8o.a deb27 . . . . . . . . . . . . . . . . . . . . . . . hem Fe
[1]1z8p.a deb27 . . . . . . . . . . . . . . . . . . S . . . . hem Fe
[1]1z8q.a deb27 . . . . . . . . . . . . . . . . . . T . . . . hem Fe

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 cF Me
S
5
9
P
6
1
F
7
2
A
7
4
Y
7
5
F
7
8
F
8
6
N
8
9
G
9
1
T
9
2
S
1
7
1
I
1
7
4
L
1
7
5
R
1
8
5
V
2
3
7
L
2
4
0
A
2
4
1
E
2
4
4
A
2
4
5
P
2
8
8
T
2
9
2
C
3
5
1
L
3
9
1
L
3
9
2
[1]1egy.a . . * . . . . . . . . . . . . . * . . . . . . . hem Fe
[1]1eup.a . . * . . . . . . . . . . . . . . . . . . . . . hem Fe
[1]1jin.a . . . . . . . . . . . . . . . . . . . . . . . . hem Fe
[1]1jip.a . . . . . . . . . . . . . . . . . . S . . . . . hem Fe
[1]1z8o.a . . * . . . . . . . * . . . . . . . . . . . . . hem Fe
[1]1z8p.a . . * . . . . . . . * . . . . . . . S . . . . . hem Fe
[1]1z8q.a . . * . . . . . . . * . . . . . . . T . . . . . hem Fe

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
1egy.a:9ap
1eup.a:asd
1jin.a:ktn
1jip.a:ktn
1z8o.a:deb
1z8p.a:deb
1z8q.a:deb
[1] 1egy.a
0
1.3 4.5 4.0 0 0 0
[1] 1eup.a 0.3
0.2
3.7 3.5 0 0 0
[1] 1jin.a 0.3 0.8
0
0 0.2 0.2 0.1
[1] 1jip.a 0.3 1.1 0.4
0.1
0 0 0
[1] 1z8o.a 0.6 1.4 3.9 3.1
0
0 0
[1] 1z8p.a 0.6 1.4 3.8 2.9 0
0
0
[1] 1z8q.a 0.5 1.6 4.3 3.4 0 0
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
1egy.a
1eup.a
1jin.a
1jip.a
1z8o.a
1z8p.a
1z8q.a
[1] 1egy.a
0
.08 .23 .23 .10 .10 .09
[1] 1eup.a .08
0
.19 .19 .08 .08 .08
[1] 1jin.a .23 .19
0
.03 .22 .21 .23
[1] 1jip.a .23 .19 .03
0
.20 .20 .21
[1] 1z8o.a .10 .08 .22 .20
0
0 .03
[1] 1z8p.a .10 .08 .21 .20 0
0
.03
[1] 1z8q.a .09 .08 .23 .21 .03 .03
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
1egy.a
1eup.a
1jin.a
1jip.a
1z8o.a
1z8p.a
1z8q.a
[1] 1egy.a
0
0.4 0.6 0.6 0.3 0.3 0.4
[1] 1eup.a 0.4
0
0.5 0.5 0.3 0.3 0.3
[1] 1jin.a 0.6 0.5
0
0.2 0.5 0.5 0.4
[1] 1jip.a 0.6 0.5 0.2
0
0.5 0.5 0.4
[1] 1z8o.a 0.3 0.3 0.5 0.5
0
0.1 0.2
[1] 1z8p.a 0.3 0.3 0.5 0.5 0.1
0
0.2
[1] 1z8q.a 0.4 0.3 0.4 0.4 0.2 0.2
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

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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
1egy.a
1eup.a
1jin.a
1jip.a
1z8o.a
1z8p.a
1z8q.a
[1] 1egy.a
0
0.6 0.9 0.9 0.7 0.7 0.7
[1] 1eup.a 0.6
0
0.9 0.8 0.6 0.6 0.6
[1] 1jin.a 0.9 0.9
0
0.5 0.8 0.8 0.8
[1] 1jip.a 0.9 0.8 0.5
0
0.8 0.8 0.8
[1] 1z8o.a 0.7 0.6 0.8 0.8
0
0.1 0.2
[1] 1z8p.a 0.7 0.6 0.8 0.8 0.1
0
0.2
[1] 1z8q.a 0.7 0.6 0.8 0.8 0.2 0.2
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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