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MYCG_MICGR_2_397

Mycinamicin IV hydroxylase/epoxidase [Cytochrome P450 family]

Composition of the binding site

Protein chains monomer
A1 (MYCG_MICGR):75, 77, 79:84, 168, 170, 174:176, 179, 187, 226, 230, 233, 234, 237, 280, 281, 284:286, 311, 386, 38775, 77, 79:84, 168, 170, 174:176, 179, 187, 226, 230, 233, 234, 237, 280, 281, 284:286, 311, 386, 387
Cofactors (cF):hem
Metals (Me):Fe

Full PDB list

2y46, 2y5n, 2y5z, 2y98, 2yca, 2ygx, 3zsn, 4aw3 (redundant Pocketome entry)

Pocket contact map

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PDB.ch
   
ligand
A1 cF Me
R
7
5
E
7
7
V
7
9
G
8
1
G
8
2
L
8
3
L
8
4
F
1
6
8
S
1
7
0
V
1
7
4
T
1
7
5
A
1
7
6
M
1
7
9
Y
1
8
7
D
2
2
6
G
2
3
0
V
2
3
3
A
2
3
4
E
2
3
7
L
2
8
0
G
2
8
1
T
2
8
4
F
2
8
6
T
3
1
1
L
3
8
6
L
3
8
7
[1]2y46.a miv49 . . . . . . . . . . . . . . . . . . . . . . . . . . hem Fe
[1]2y5n.a myv50 . . . . . . . . . . . . . . . . . . . . . . . . . . hem Fe
[1]2yca.a zm348 . . . . . . . . . . . . . . . . . . . . . . . . . . hem Fe
[1]2ygx.c none . . . . . . . . . . . . . . . . . . . . . . . . . . hem Fe
[1]3zsn.a miv49 . . . . . . . . . . . . . . . . . . . . . . A . . . hem Fe
[1]4aw3.a myv50 . . . . . . . . . . . . . . . . . . . . . . V . . . 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

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PDB.ch
A1 cF Me
R
7
5
E
7
7
V
7
9
K
8
0
G
8
1
G
8
2
L
8
3
L
8
4
F
1
6
8
S
1
7
0
V
1
7
4
T
1
7
5
A
1
7
6
M
1
7
9
Y
1
8
7
D
2
2
6
G
2
3
0
V
2
3
3
A
2
3
4
E
2
3
7
L
2
8
0
G
2
8
1
T
2
8
4
A
2
8
5
F
2
8
6
T
3
1
1
L
3
8
6
L
3
8
7
[1]2y46.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . hem Fe
[1]2y5n.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . hem Fe
[1]2yca.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . hem Fe
[1]2ygx.c * . . . . . . . . . . . . . . . . . . . . . . . . . . . hem Fe
[1]3zsn.a . . . . . . . . . . . . . . . . . . . . . . . . A . . . hem Fe
[1]4aw3.a . . . . . . . . . . . . . . . . . . . . . . . . V . . . 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
2y46.a:miv
2y5n.a:myv
2yca.a:zm3
2ygx.c is apo
3zsn.a:miv
4aw3.a:myv
[1] 2y46.a
0
0 0.5 - 0 0.7
[1] 2y5n.a 0
0
0.6 - 0 0.7
[1] 2yca.a 0.9 1.2
0
- 0.9 0.7
[1] 2ygx.c 1.4 1.5 0.8
-
1.4 1.9
[1] 3zsn.a 0 0 0.3 -
0
0.1
[1] 4aw3.a 0 0 0.1 - 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
2y46.a
2y5n.a
2yca.a
2ygx.c
3zsn.a
4aw3.a
[1] 2y46.a
0
0 .07 .08 .03 .04
[1] 2y5n.a 0
0
.07 .08 .03 .04
[1] 2yca.a .07 .07
0
.06 .06 .06
[1] 2ygx.c .08 .08 .06
0
.09 .10
[1] 3zsn.a .03 .03 .06 .09
0
.02
[1] 4aw3.a .04 .04 .06 .10 .02
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.9 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
2y46.a
2y5n.a
2yca.a
2ygx.c
3zsn.a
4aw3.a
[1] 2y46.a
0
0.3 1.1 0.6 0.7 0.8
[1] 2y5n.a 0.3
0
1.1 0.7 0.8 0.8
[1] 2yca.a 1.1 1.1
0
0.9 0.7 0.8
[1] 2ygx.c 0.6 0.7 0.9
0
0.7 0.8
[1] 3zsn.a 0.7 0.8 0.7 0.7
0
0.6
[1] 4aw3.a 0.8 0.8 0.8 0.8 0.6
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.7 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
2y46.a
2y5n.a
2yca.a
2ygx.c
3zsn.a
4aw3.a
[1] 2y46.a
0
0.5 1.3 0.7 0.8 0.9
[1] 2y5n.a 0.5
0
1.4 0.8 0.8 1.0
[1] 2yca.a 1.3 1.4
0
1.2 1.1 1.1
[1] 2ygx.c 0.7 0.8 1.2
0
0.9 1.0
[1] 3zsn.a 0.8 0.8 1.1 0.9
0
0.7
[1] 4aw3.a 0.9 1.0 1.1 1.0 0.7
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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