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CP11A_HUMAN_42_519

Cholesterol side-chain cleavage enzyme, mitochondrial [Cytochrome P450 family]

Composition of the binding site

Protein chains monomer
A1 (CP11A_HUMAN):120, 121, 123, 126, 140, 240, 241, 322, 325, 326, 330, 390:393, 395, 497, 499, 500120, 121, 123, 126, 140, 240, 241, 322, 325, 326, 330, 390:393, 395, 497, 499, 500
Cofactors (cF):hem
Metals (Me):Fe

Full PDB list

3n9y, 3n9z, 3na0, 3na1

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 cF Me
R
1
2
0
F
1
2
1
I
1
2
3
W
1
2
6
L
1
4
0
M
2
4
0
F
2
4
1
E
3
2
2
A
3
2
5
G
3
2
6
T
3
3
0
S
3
9
1
V
3
9
2
T
3
9
3
Q
3
9
5
F
4
9
7
L
4
9
9
I
5
0
0
[1]3n9y.a clr28 . . . . . . . . . . . . . . . . . . hem Fe
[1]3n9z.a hc929 . . . . . . . . . . . . . . . . . . hem Fe
[1]3na0.b 2dc30 . . . . . . . . . . . . . . . . . . hem Fe
[1]3na1.a hcd29 . . . . . . . . . . . . . . . . . . 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
1
2
0
F
1
2
1
I
1
2
3
W
1
2
6
L
1
4
0
M
2
4
0
F
2
4
1
E
3
2
2
A
3
2
5
G
3
2
6
T
3
3
0
I
3
9
0
S
3
9
1
V
3
9
2
T
3
9
3
Q
3
9
5
F
4
9
7
L
4
9
9
I
5
0
0
[1]3n9y.a . . . . . . . . . . . . . . . . . . . hem Fe
[1]3n9z.a . . . . . . . . . . . . . . . . . . . hem Fe
[1]3na0.b . . . . . . . . . . . . . . . . . . . hem Fe
[1]3na1.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
3n9y.a:clr
3n9z.a:hc9
3na0.b:2dc
3na1.a:hcd
[1] 3n9y.a
0
0 0 0
[1] 3n9z.a 0
0
0 0
[1] 3na0.b 0 0
0
0
[1] 3na1.a 0 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
3n9y.a
3n9z.a
3na0.b
3na1.a
[1] 3n9y.a
0
0 0 0
[1] 3n9z.a 0
0
0 0
[1] 3na0.b 0 0
0
0
[1] 3na1.a 0 0 0
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.3 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
3n9y.a
3n9z.a
3na0.b
3na1.a
[1] 3n9y.a
0
0.2 0.1 0.2
[1] 3n9z.a 0.2
0
0.2 0.2
[1] 3na0.b 0.1 0.2
0
0.2
[1] 3na1.a 0.2 0.2 0.2
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.2 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
3n9y.a
3n9z.a
3na0.b
3na1.a
[1] 3n9y.a
0
0.4 0.4 0.4
[1] 3n9z.a 0.4
0
0.3 0.3
[1] 3na0.b 0.4 0.3
0
0.3
[1] 3na1.a 0.4 0.3 0.3
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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