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CP24A_RAT_33_514_catalytic

1,25-dihydroxyvitamin D(3) 24-hydroxylase, mitochondrial [Cytochrome P450 family]

Composition of the binding site

Protein chains monomer
A1 (CP24A_RAT):79, 128, 131, 134, 148, 204, 205, 208, 243, 246, 247, 249, 251, 253, 254, 326, 329, 391, 393, 394, 498:50079, 128, 131, 134, 148, 204, 205, 208, 243, 246, 247, 249, 251, 253, 254, 326, 329, 391, 393, 394, 498:500
Cofactors (cF):hem
Metals (Me):Fe

Full PDB list

3k9v, 3k9y

Pocket contact map

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PDB.ch
   
ligand
A1 cF Me
R
1
2
8
W
1
3
4
M
1
4
8
Y
2
0
4
S
2
0
5
N
2
0
8
K
2
4
3
M
2
4
6
S
2
4
7
F
2
4
9
K
2
5
1
M
2
5
3
V
2
5
4
E
3
2
9
V
3
9
1
T
3
9
4
L
4
9
8
G
4
9
9
I
5
0
0
[1]3k9v.a cps42 . . . . . . . . . . . . . . . . . . . hem Fe
[1]3k9y.a cm534 . . . . . . . . . . . . . . . . . . . hem Fe
[1]3k9y.b none . . . . . . . . . . . . . . . . . . . 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
L
7
9
R
1
2
8
I
1
3
1
W
1
3
4
M
1
4
8
Y
2
0
4
S
2
0
5
N
2
0
8
K
2
4
3
M
2
4
6
S
2
4
7
F
2
4
9
K
2
5
1
M
2
5
3
V
2
5
4
A
3
2
6
E
3
2
9
V
3
9
1
F
3
9
3
T
3
9
4
L
4
9
8
G
4
9
9
I
5
0
0
[1]3k9v.a . . . . . . . . . . . . . . . . . . . . . . . hem Fe
[1]3k9y.a . . . . . . . . . . . . . . . . . . . . . . . hem Fe
[1]3k9y.b . . . . . . . . . . . . . . . . . . . . . . . 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
3k9v.a:cps
3k9y.a:cm5
3k9y.b is apo
[1] 3k9v.a
0
0 -
[1] 3k9y.a 0.6
0
-
[1] 3k9y.b 0.7 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
3k9v.a
3k9y.a
3k9y.b
[1] 3k9v.a
0
.03 .03
[1] 3k9y.a .03
0
0
[1] 3k9y.b .03 0
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
3k9v.a
3k9y.a
3k9y.b
[1] 3k9v.a
0
0.7 0.8
[1] 3k9y.a 0.7
0
0.7
[1] 3k9y.b 0.8 0.7
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.7 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
3k9v.a
3k9y.a
3k9y.b
[1] 3k9v.a
0
0.9 1.0
[1] 3k9y.a 0.9
0
0.9
[1] 3k9y.b 1.0 0.9
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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