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CP130_MYCTU_2_405

Cytochrome P450 130 [Cytochrome P450 family]

Composition of the binding site

Protein chains monomer
A1 (CP130_MYCTU):71, 83, 85:91, 177, 194, 231, 234:236, 238, 239, 242:244, 247, 290, 293, 392, 39371, 83, 85:91, 177, 194, 231, 234:236, 238, 239, 242:244, 247, 290, 293, 392, 393
Cofactors (cF):hem
Metals (Me):Fe

Full PDB list

2uuq, 2uvn, 2wgy, 2wh8, 2whf

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 cF Me
L
7
1
L
8
3
D
8
5
T
8
6
P
8
7
P
8
8
M
8
9
V
9
0
M
9
1
N
1
7
7
A
2
3
5
F
2
3
6
F
2
3
8
T
2
3
9
T
2
4
2
G
2
4
3
G
2
4
4
T
2
4
7
V
2
9
0
L
2
9
3
Y
3
9
2
V
3
9
3
[1]2uuq.a none . . . . . . . . . . . . . . . . . . . . . . hem Fe
[1]2wgy.a none . . . . . . . . . . . . . . . A . . . . . . hem Fe
[1]2wh8.a ii226 . . . . . . . . . . . . . . . . . . . . . . hem Fe
[1]2whf.a ii4,ii434 . . . . . . . . . . . . . . . . . . . . . . hem Fe
[2]2uvn.a ecn24 . . . . . . . . . . . . . . . . . . . . . . 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
L
7
1
L
8
3
D
8
5
T
8
6
P
8
7
P
8
8
M
8
9
V
9
0
M
9
1
N
1
7
7
M
1
9
4
L
2
3
1
L
2
3
4
A
2
3
5
F
2
3
6
F
2
3
8
T
2
3
9
T
2
4
2
G
2
4
3
G
2
4
4
T
2
4
7
V
2
9
0
L
2
9
3
Y
3
9
2
V
3
9
3
[1]2uuq.a . . . . . . . . . . . . . . . * * . * . . . . . . hem Fe
[1]2wgy.a . . . . . . . . . . . . . . . * . . A . . . . . . hem Fe
[1]2wh8.a . . . . . . . . . . . . . . . . . . . . . . . . . hem Fe
[1]2whf.a . . . . . . . * . . . . . . . . . . . . . . . . . hem Fe
[2]2uvn.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
2uuq.a is apo
2wgy.a is apo
2wh8.a:ii2
2whf.a:ii4
2uvn.a:ecn
[1] 2uuq.a
-
- 0.9 1.2 2.8
[1] 2wgy.a -
-
1.1 1.4 3.2
[1] 2wh8.a - -
0.1
0.1 2.4
[1] 2whf.a - - 0
0.2
2.9
[2] 2uvn.a - - 7.7 9.0
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
2uuq.a
2wgy.a
2wh8.a
2whf.a
2uvn.a
[1] 2uuq.a
0
.04 .06 .07 .46
[1] 2wgy.a .04
0
.09 .08 .48
[1] 2wh8.a .06 .09
0
.03 .40
[1] 2whf.a .07 .08 .03
0
.43
[2] 2uvn.a .46 .48 .40 .43
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
2uuq.a
2wgy.a
2wh8.a
2whf.a
2uvn.a
[1] 2uuq.a
0
0.7 0.5 0.3 6.1
[1] 2wgy.a 0.7
0
0.7 0.6 6.1
[1] 2wh8.a 0.5 0.7
0
0.3 6.2
[1] 2whf.a 0.3 0.6 0.3
0
6.2
[2] 2uvn.a 6.1 6.1 6.2 6.2
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.6 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
2uuq.a
2wgy.a
2wh8.a
2whf.a
2uvn.a
[1] 2uuq.a
0
0.8 1.1 0.6 6.0
[1] 2wgy.a 0.8
0
1.2 0.9 6.3
[1] 2wh8.a 1.1 1.2
0
0.9 6.5
[1] 2whf.a 0.6 0.9 0.9
0
6.6
[2] 2uvn.a 6.0 6.3 6.5 6.6
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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