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CPXE_STRGO_1_406

Vitamin D3 dihydroxylase [Cytochrome P450 family]

Composition of the binding site

Protein chains monomer
A1 (CPXE_STRGO):73, 78:81, 84, 85, 87, 88, 91, 92, 180, 181, 193, 236, 239, 243, 293, 294, 296, 394:39673, 78:81, 84, 85, 87, 88, 91, 92, 180, 181, 193, 236, 239, 243, 293, 294, 296, 394:396
Cofactors (cF):hem
Metals (Me):Fe

Full PDB list

2zbx, 2zby, 2zbz, 3cv8, 3cv9, 5x7e

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 cF Me
R
7
3
F
7
8
P
7
9
T
8
1
R
8
4
F
8
5
V
8
8
S
9
1
P
9
2
L
1
8
0
V
1
8
1
R
1
9
3
S
2
3
6
M
2
3
9
I
2
4
3
I
2
9
3
A
2
9
4
G
2
9
6
T
3
9
4
T
3
9
5
I
3
9
6
[1]2zbx.a none . . . . . . - . . . . . . . . . . . . . . hem Fe
[1]2zby.a none . . . . A . . . . . . . . . . . . . . . . hem Fe
[1]2zbz.a vdx30 . . . . A . . . . . . . . . . . . . . . . hem Fe
[1]3cv9.a vdx30 A . . . A . . . . . . . . . . . . . . . . hem Fe
[1]5x7e.a 7zu31 . . . . A . . . . . . . . . . . . . . . . hem Fe
[2]3cv8.a none . . . . F . . . . . . . . . . . . . . . . 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
R
7
3
F
7
8
P
7
9
A
8
0
T
8
1
R
8
4
F
8
5
A
8
7
V
8
8
S
9
1
P
9
2
L
1
8
0
V
1
8
1
R
1
9
3
S
2
3
6
M
2
3
9
I
2
4
3
I
2
9
3
A
2
9
4
G
2
9
6
T
3
9
4
T
3
9
5
I
3
9
6
[1]2zbx.a . . . . . * . - - . . . . . . . . * . . . . . hem Fe
[1]2zby.a . . . . . A . . . . . . . . . . . * . . . . . hem Fe
[1]2zbz.a . . . . . A . . . . . . . . . . . . . . . . . hem Fe
[1]3cv9.a A . . . . A . . . . . . . . . . . . . . . . . hem Fe
[1]5x7e.a . . . . . A . . . . . . . . . . . . . . . . . hem Fe
[2]3cv8.a . . . . . F * . . . . . . . . . . . . . . . . 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
2zbx.a is apo
2zby.a is apo
2zbz.a:vdx
3cv9.a:vdx
5x7e.a:7zu
3cv8.a is apo
[1] 2zbx.a
-
- 4.8 2.9 1.7 -
[1] 2zby.a -
-
4.4 3.1 3.0 -
[1] 2zbz.a - -
0
0.2 0.4 -
[1] 3cv9.a - - 0.2
0
0.1 -
[1] 5x7e.a - - 0.3 0
0
-
[2] 3cv8.a - - 4.5 5.2 5.2
-
[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
2zbx.a
2zby.a
2zbz.a
3cv9.a
5x7e.a
3cv8.a
[1] 2zbx.a
0
.13 .23 .20 .20 .32
[1] 2zby.a .13
0
.20 .21 .21 .36
[1] 2zbz.a .23 .20
0
.02 .03 .22
[1] 3cv9.a .20 .21 .02
0
.01 .23
[1] 5x7e.a .20 .21 .03 .01
0
.23
[2] 3cv8.a .32 .36 .22 .23 .23
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.0 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
2zbx.a
2zby.a
2zbz.a
3cv9.a
5x7e.a
3cv8.a
[1] 2zbx.a
0
0.8 0.8 0.8 0.9 1.1
[1] 2zby.a 0.8
0
0.8 0.8 1.0 1.2
[1] 2zbz.a 0.8 0.8
0
0.3 0.7 0.9
[1] 3cv9.a 0.8 0.8 0.3
0
0.7 1.0
[1] 5x7e.a 0.9 1.0 0.7 0.7
0
0.6
[2] 3cv8.a 1.1 1.2 0.9 1.0 0.6
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.8 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
2zbx.a
2zby.a
2zbz.a
3cv9.a
5x7e.a
3cv8.a
[1] 2zbx.a
0
0.9 1.1 1.0 1.1 1.6
[1] 2zby.a 0.9
0
1.1 1.1 1.3 1.6
[1] 2zbz.a 1.1 1.1
0
0.4 0.8 1.1
[1] 3cv9.a 1.0 1.1 0.4
0
0.8 1.2
[1] 5x7e.a 1.1 1.3 0.8 0.8
0
1.0
[2] 3cv8.a 1.6 1.6 1.1 1.2 1.0
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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