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CPVDH_PSEAH_1_403

Vitamin D(3) 25-hydroxylase [Cytochrome P450 family]

Composition of the binding site

Protein chains monomer
A1 (CPVDH_PSEAH):67, 83, 84, 86, 88, 89, 171, 172, 180, 181, 184, 232, 235, 236, 240, 283, 287, 288, 290, 38767, 83, 84, 86, 88, 89, 171, 172, 180, 181, 184, 232, 235, 236, 240, 283, 287, 288, 290, 387
Cofactors (cF):hem
Metals (Me):Fe

Full PDB list

3a4g, 3a4h, 3a4z, 3a50, 3a51, 3vrm, 5gnl, 5gnm (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 cF Me
T
8
4
M
8
6
I
8
8
L
8
9
L
1
7
1
V
1
7
2
K
1
8
0
N
1
8
1
M
1
8
4
L
2
3
2
I
2
3
5
A
2
3
6
T
2
4
0
V
2
8
3
P
2
8
7
L
3
8
7
[1]3a4g.a pg08 . . . . . . . . . . . . . . . . hem Fe
[1]3a4z.c none . . . . . . . . . . . . . . . . hem Fe
[1]3a50.c vd328 . . . . . . . . . . . . . . . . hem Fe
[1]3a51.c vdy29 . . . . . . . . . . . . . . . . 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
W
6
7
P
8
3
T
8
4
M
8
6
I
8
8
L
8
9
L
1
7
1
V
1
7
2
K
1
8
0
N
1
8
1
M
1
8
4
L
2
3
2
I
2
3
5
A
2
3
6
T
2
4
0
V
2
8
3
P
2
8
7
I
2
8
8
F
2
9
0
L
3
8
7
[1]3a4g.a . . . . . . . . . . . . . . . . . . . . hem Fe
[1]3a4z.c . . . . . . . . . . . . . . . . . . . . hem Fe
[1]3a50.c . . . . . . . . . . . . . . . . . . . . hem Fe
[1]3a51.c . . . . . . . . . . . . . . . . . . . . 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
3a4g.a:pg0
3a4z.c is apo
3a50.c:vd3
3a51.c:vdy
[1] 3a4g.a
0
- 0.2 0.4
[1] 3a4z.c 0
-
0 0
[1] 3a50.c 0 -
0
0
[1] 3a51.c 0.2 - 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
3a4g.a
3a4z.c
3a50.c
3a51.c
[1] 3a4g.a
0
.02 .02 .03
[1] 3a4z.c .02
0
0 .01
[1] 3a50.c .02 0
0
.01
[1] 3a51.c .03 .01 .01
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.2 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
3a4g.a
3a4z.c
3a50.c
3a51.c
[1] 3a4g.a
0
3.2 3.2 3.2
[1] 3a4z.c 3.2
0
0.1 0.1
[1] 3a50.c 3.2 0.1
0
0.2
[1] 3a51.c 3.2 0.1 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
3a4g.a
3a4z.c
3a50.c
3a51.c
[1] 3a4g.a
0
3.3 3.3 3.3
[1] 3a4z.c 3.3
0
0.1 0.2
[1] 3a50.c 3.3 0.1
0
0.2
[1] 3a51.c 3.3 0.2 0.2
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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