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CP2B4_RABIT_22_491_peripheralTMI

Cytochrome P450 2B4 [Cytochrome P450 family]

Composition of the binding site

Protein chains monomer
A1 (CP2B4_RABIT):107, 108, 183, 184, 198, 201, 202, 205, 234, 236:242, 244, 245, 287, 290:294, 296, 297107, 108, 183, 184, 198, 201, 202, 205, 234, 236:242, 244, 245, 287, 290:294, 296, 297
Metals (Me):Fe

Full PDB list

1po5, 1suo, 2bdm, 2q6n, 3g5n, 3g93, 3kw4, 3me6, 3mvr, 3r1a, 3r1b, 3tk3, 3tmz, 3uas, 4h1n, 4jlt, 4mgj, 5em4, 5iut, 5iuz (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
F
1
8
4
L
1
9
8
L
2
0
1
F
2
0
2
L
2
3
8
I
2
4
1
I
2
4
5
N
2
8
7
L
2
9
0
T
2
9
1
L
2
9
3
S
2
9
4
F
2
9
7
[1]4h1n.a none . . . . . . . . . . . . A Fe
[1]5em4.a none . . . . . . . . . . . . . Fe
[2]3r1a.a none . . . . . . . . . . . . . Fe
[2]5iut.a none . . . W . . . . . . . . . Fe
[3]2bdm.a tmi24 . . . . . . . . . . . . .

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 Me
I
1
0
7
F
1
0
8
V
1
8
3
F
1
8
4
L
1
9
8
L
2
0
1
F
2
0
2
S
2
0
5
I
2
3
4
R
2
3
6
N
2
3
7
L
2
3
8
Q
2
3
9
E
2
4
0
I
2
4
1
N
2
4
2
F
2
4
4
I
2
4
5
N
2
8
7
L
2
9
0
T
2
9
1
V
2
9
2
L
2
9
3
S
2
9
4
F
2
9
6
F
2
9
7
[1]4h1n.a . . . . . . . . . . . * . . . . . . . . . . * . . A Fe
[1]5em4.a . . . . . . . . . . . * . . . . W . . * . . * . * . Fe
[2]3r1a.a . . . . . . . . . . . * . . * * . . . . . . * . * . Fe
[2]5iut.a . . . . . . W . . . . * . . * * . . . . . . * . . . Fe
[3]2bdm.a . . . . . . . . . . . . . . . . . . . . . . . . . .

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
4h1n.a is apo
5em4.a is apo
3r1a.a is apo
5iut.a is apo
2bdm.a:tmi
[1] 4h1n.a
-
- - - 8.4
[1] 5em4.a -
-
- - 9.4
[2] 3r1a.a - -
-
- 12
[2] 5iut.a - - -
-
11
[3] 2bdm.a - - - -
0
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (3 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
4h1n.a
5em4.a
3r1a.a
5iut.a
2bdm.a
[1] 4h1n.a
0
.04 .25 .28 .30
[1] 5em4.a .04
0
.24 .28 .34
[2] 3r1a.a .25 .24
0
.14 .43
[2] 5iut.a .28 .28 .14
0
.39
[3] 2bdm.a .30 .34 .43 .39
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 2.0 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
4h1n.a
5em4.a
3r1a.a
5iut.a
2bdm.a
[1] 4h1n.a
0
0.4 1.5 1.9 9.1
[1] 5em4.a 0.4
0
1.6 1.9 9.0
[2] 3r1a.a 1.5 1.6
0
1.1 9.3
[2] 5iut.a 1.9 1.9 1.1
0
9.3
[3] 2bdm.a 9.1 9.0 9.3 9.3
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 1.6 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
4h1n.a
5em4.a
3r1a.a
5iut.a
2bdm.a
[1] 4h1n.a
0
0.6 1.9 2.0 11
[1] 5em4.a 0.6
0
2.0 2.1 11
[2] 3r1a.a 1.9 2.0
0
1.5 11
[2] 5iut.a 2.0 2.1 1.5
0
11
[3] 2bdm.a 11 11 11 11
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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