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CP24A_RAT_33_514_peripheralCPS

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

Composition of the binding site

Protein chains monomer
A1 (CP24A_RAT):70, 74, 79, 82, 101, 104, 129, 130, 132, 246, 247, 249, 251, 253, 254, 393, 497, 49970, 74, 79, 82, 101, 104, 129, 130, 132, 246, 247, 249, 251, 253, 254, 393, 497, 499
Cofactors (cF):hem
Metals (Me):Fe

Full PDB list

3k9v, 3k9y

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 cF Me
L
7
0
F
7
4
L
7
9
Q
8
2
L
1
0
1
F
1
0
4
L
1
2
9
K
1
3
2
M
2
4
6
S
2
4
7
F
2
4
9
K
2
5
1
M
2
5
3
V
2
5
4
F
3
9
3
H
4
9
7
[1]3k9v.a cps32 . . . . . . . . . . . . . . . . hem Fe
[1]3k9y.a cm5,cm568 . . . . . . . . . . . . . . . . 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
0
F
7
4
L
7
9
Q
8
2
L
1
0
1
F
1
0
4
L
1
2
9
E
1
3
0
K
1
3
2
M
2
4
6
S
2
4
7
F
2
4
9
K
2
5
1
M
2
5
3
V
2
5
4
F
3
9
3
H
4
9
7
G
4
9
9
[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
0.4 -
[1] 3k9y.a 0.2
0.1
-
[1] 3k9y.b 0.7 0.3
-
[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
.04 .07
[1] 3k9y.a .04
0
.04
[1] 3k9y.b .07 .04
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
3k9v.a
3k9y.a
3k9y.b
[1] 3k9v.a
0
0.8 1.1
[1] 3k9y.a 0.8
0
0.9
[1] 3k9y.b 1.1 0.9
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.9 Å)

Pockets (x) vs pockets (y) colored by RMSD of all site residue atoms

zoom: [−] [+]; [view as image]; [download as text]

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
1.0 1.3
[1] 3k9y.a 1.0
0
1.1
[1] 3k9y.b 1.3 1.1
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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