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ERYK_SACEN_1_397

Erythromycin C-12 hydroxylase [Cytochrome P450 family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (ERYK_SACEN):R: Substrate binding (74, 75)
69, 72, 73, 155, 158:161, 163, 172, 176, 223, 226:228, 230, 231, 274, 276:278, 299, 377:379
69, 72:75, 155, 158:161, 163, 172, 176, 223, 226:228, 230, 231, 274, 276:278, 299, 377:379
Cofactors (cF):hem
Metals (Me):Fe

Full PDB list

2jjn, 2jjo, 2jjp, 2wio, 2xfh, 3zkp (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 cF Me
M
7
2
I
7
3
H
7
4
E
7
5
L
1
5
5
I
1
5
8
Q
1
5
9
M
1
6
0
P
1
6
3
I
1
7
2
L
1
7
6
A
2
2
3
L
2
2
6
A
2
2
7
I
2
3
0
T
2
3
1
F
2
7
4
Q
2
7
6
Q
2
7
8
I
3
7
8
V
3
7
9
[1]2jjn.a none . . . . . . . . . . . . . . . . . . . . . hem Fe
[1]2jjo.a ey549 . . . . . . . . . . . . . . . . . . . . . hem Fe
[1]2jjp.a kln36 . . . . . . . . . . . . . . . . . . . . . hem Fe
[1]2xfh.a cl625 . . . . . . . . . . . . . . . . . . . . . hem Fe
[1]3zkp.a erb50 A . . . . . . . . . . . . . . . . . . . . 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
T
6
9
M
7
2
I
7
3
H
7
4
E
7
5
L
1
5
5
I
1
5
8
Q
1
5
9
M
1
6
0
D
1
6
1
P
1
6
3
I
1
7
2
L
1
7
6
A
2
2
3
L
2
2
6
A
2
2
7
G
2
2
8
I
2
3
0
T
2
3
1
F
2
7
4
Q
2
7
6
M
2
7
7
Q
2
7
8
N
2
9
9
Q
3
7
7
I
3
7
8
V
3
7
9
[1]2jjn.a . . . . . . . . . . . . . . . . . . . * . . . . . . . hem Fe
[1]2jjo.a . . . . . . . . . . . . . . . . . . . * . . . . . . . hem Fe
[1]2jjp.a . . . . . . . . . . . . . . . . . . . * . . . . . . . hem Fe
[1]2xfh.a . . . . . . . . . . . . . . . . . . . * . . . . . . . hem Fe
[1]3zkp.a . A . . . . . . . . . . . . . . . . . * . . . . . . . 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
2jjn.a is apo
2jjo.a:ey5
2jjp.a:kln
2xfh.a:cl6
3zkp.a:erb
[1] 2jjn.a
-
3.7 2.8 1.7 3.5
[1] 2jjo.a -
0.1
2.3 1.9 0
[1] 2jjp.a - 2.8
0
0.5 2.8
[1] 2xfh.a - 2.2 0.4
0
2.5
[1] 3zkp.a - 0.1 1.9 1.9
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
2jjn.a
2jjo.a
2jjp.a
2xfh.a
3zkp.a
[1] 2jjn.a
0
.14 .13 .16 .14
[1] 2jjo.a .14
0
.11 .11 .01
[1] 2jjp.a .13 .11
0
.07 .09
[1] 2xfh.a .16 .11 .07
0
.10
[1] 3zkp.a .14 .01 .09 .10
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 2.0 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
2jjn.a
2jjo.a
2jjp.a
2xfh.a
3zkp.a
[1] 2jjn.a
0
1.6 1.6 4.0 1.5
[1] 2jjo.a 1.6
0
1.3 3.8 0.4
[1] 2jjp.a 1.6 1.3
0
3.9 1.2
[1] 2xfh.a 4.0 3.8 3.9
0
4.0
[1] 3zkp.a 1.5 0.4 1.2 4.0
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 1.5 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
2jjn.a
2jjo.a
2jjp.a
2xfh.a
3zkp.a
[1] 2jjn.a
0
2.1 2.0 4.6 2.0
[1] 2jjo.a 2.1
0
1.8 4.6 0.5
[1] 2jjp.a 2.0 1.8
0
4.8 1.7
[1] 2xfh.a 4.6 4.6 4.8
0
4.8
[1] 3zkp.a 2.0 0.5 1.7 4.8
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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