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CP125_MYCTU_7_433

Steroid C26-monooxygenase [Cytochrome P450 family]

Composition of the binding site

Protein chains monomer
A1 (CP125_MYCTU):97, 100, 104, 108, 111, 112, 114, 115, 117, 200:202, 213, 214, 217, 218, 221, 259, 260, 263, 264, 267, 268, 272, 316, 41497, 100, 104, 108, 111, 112, 114, 115, 117, 200:202, 213, 214, 217, 218, 221, 259, 260, 263, 264, 267, 268, 272, 316, 414
Cofactors (cF):hem
Metals (Me):Fe

Full PDB list

2x5l, 2x5w, 2xc3, 2xn8, 3ivy, 3iw0, 3iw1, 3iw2 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 cF Me
I
9
7
F
1
0
0
I
1
0
4
D
1
0
8
V
1
1
1
Q
1
1
2
F
1
1
4
V
1
1
5
L
1
1
7
M
2
0
0
T
2
0
1
G
2
0
2
P
2
1
3
K
2
1
4
S
2
1
7
A
2
1
8
I
2
2
1
F
2
6
0
V
2
6
3
M
2
6
4
V
2
6
7
A
2
6
8
T
2
7
2
F
3
1
6
W
4
1
4
[1]2xc3.a rt830 . . . . . . . . . . . . . . . . . . . . . . . . . hem Fe
[1]3ivy.a none . . . . . . . . . . . . . . . . . . . . . . . . . hem Fe
[1]3iw1.a asd21 . . . . . . . . . . . . . . . . . . . . . . . . . hem Fe
[1]3iw2.a eko24 . . . . . . . . . . . . . . . . . . . . . . . . . hem Fe
[2]2x5w.a k2b28 . . . . . . . . . . . . . . . . . . . . . . . . . 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
I
9
7
F
1
0
0
I
1
0
4
D
1
0
8
V
1
1
1
Q
1
1
2
F
1
1
4
V
1
1
5
L
1
1
7
M
2
0
0
T
2
0
1
G
2
0
2
P
2
1
3
K
2
1
4
S
2
1
7
A
2
1
8
I
2
2
1
G
2
5
9
F
2
6
0
V
2
6
3
M
2
6
4
V
2
6
7
A
2
6
8
T
2
7
2
F
3
1
6
W
4
1
4
[1]2xc3.a . . . . . . . . . . . . . . . . . . . . . . . . . . hem Fe
[1]3ivy.a . . . . . * . . . . . . . . . . . . . . . . . . . . hem Fe
[1]3iw1.a . . . . . * . . . . . . . . . . . . . . . . . . . . hem Fe
[1]3iw2.a . . . . . * . . . . . . . . . . . . . . . * . . . . hem Fe
[2]2x5w.a . . . . . . . . . . . . . . . . * . * * . . . . . . 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
2xc3.a:rt8
3ivy.a is apo
3iw1.a:asd
3iw2.a:eko
2x5w.a:k2b
[1] 2xc3.a
0
- 0.1 0.8 0.8
[1] 3ivy.a 1.6
-
0.2 1.0 1.4
[1] 3iw1.a 1.7 -
0
1.6 1.7
[1] 3iw2.a 1.4 - 0.1
0.1
1.0
[2] 2x5w.a 4.6 - 4.2 5.5
0
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (2 clusters)

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
2xc3.a
3ivy.a
3iw1.a
3iw2.a
2x5w.a
[1] 2xc3.a
0
.09 .11 .07 .28
[1] 3ivy.a .09
0
.04 .06 .27
[1] 3iw1.a .11 .04
0
.08 .29
[1] 3iw2.a .07 .06 .08
0
.28
[2] 2x5w.a .28 .27 .29 .28
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.8 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
2xc3.a
3ivy.a
3iw1.a
3iw2.a
2x5w.a
[1] 2xc3.a
0
0.6 0.6 0.5 2.2
[1] 3ivy.a 0.6
0
0.2 0.4 1.9
[1] 3iw1.a 0.6 0.2
0
0.4 1.9
[1] 3iw2.a 0.5 0.4 0.4
0
2.0
[2] 2x5w.a 2.2 1.9 1.9 2.0
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.5 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
2xc3.a
3ivy.a
3iw1.a
3iw2.a
2x5w.a
[1] 2xc3.a
0
0.8 0.9 0.8 2.1
[1] 3ivy.a 0.8
0
0.6 0.7 2.0
[1] 3iw1.a 0.9 0.6
0
0.7 2.0
[1] 3iw2.a 0.8 0.7 0.7
0
2.0
[2] 2x5w.a 2.1 2.0 2.0 2.0
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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