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PIKC_STRVZ_2_416

Cytochrome P450 monooxygenase PikC [Cytochrome P450 family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (PIKC_STRVZ):R: Substrate binding (187, 188, 191)
R: Substrate binding (238, 239, 242:244, 246)
48, 50, 74, 81, 85, 88, 89, 93, 94, 178:180, 194, 247, 290, 292, 294, 295, 392, 394, 395
48, 50, 74, 81, 85, 88, 89, 93, 94, 178:180, 187, 188, 191, 194, 238, 239, 242:244, 246, 247, 290, 292, 294, 295, 392, 394, 395
Cofactors (cF):hem
Metals (Me):Fe

Full PDB list

2bvj, 2c6h, 2c7x, 2ca0, 2cd8, 2vz7, 2vzm, 2whw, 2wi9, 3zk5, 3zpi, 4b7d, 4b7s, 4umz (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 cF Me
D
5
0
W
7
4
L
8
1
E
8
5
L
8
8
N
8
9
L
9
3
E
9
4
F
1
7
8
V
1
7
9
A
1
8
7
M
1
9
1
M
1
9
4
H
2
3
8
I
2
3
9
V
2
4
2
A
2
4
3
E
2
4
6
T
2
4
7
V
2
9
0
T
2
9
4
Y
2
9
5
N
3
9
2
M
3
9
4
I
3
9
5
[1]2bvj.a none . . . . . . . . . . . . . . . . . . . . . . . . . hem Fe
[1]2c7x.a nrb36 . . . . . . . . . . . . . . . . . . . . . . . . . hem Fe
[1]2cd8.b pxi32 . . . . . . . . . . . . . . . . . . . . . . . . . hem Fe
[1]2vz7.a pxi32 N . . . . . . . . . . . . . . . . . . . . . . . . hem Fe
[1]2vzm.a nrb36 N . . . . . . . . . . . . . . . . . . . . . . . . hem Fe
[1]2whw.b 1d425 N . . . . . . . . . . . . . . . . . . . . . . . . hem Fe
[1]2wi9.a 1d224 N . . . . . . . . . . . . . . . . . . . . . . . . hem Fe
[1]3zk5.b z1827 N . . . . . . . . . . . . . . . . . . . . . . . . hem Fe
[1]3zpi.a none N . . . . . . . . . . . . . . . . . . . . . . . . hem Fe
[1]4b7d.a qle28 . . . . . . . . . . . . . . . . . . . . . . . . . Fe
[1]4b7s.a qle28 N . . . . . . . . . . . . . . . . . . . . . . . . hem Fe
[1]4umz.a xjo33 N . . . . . . . . . . . . . . . . . . . . . . . . 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
E
4
8
D
5
0
W
7
4
L
8
1
E
8
5
L
8
8
N
8
9
L
9
3
E
9
4
F
1
7
8
V
1
7
9
F
1
8
0
A
1
8
7
Q
1
8
8
M
1
9
1
M
1
9
4
H
2
3
8
I
2
3
9
V
2
4
2
A
2
4
3
G
2
4
4
E
2
4
6
T
2
4
7
V
2
9
0
S
2
9
2
T
2
9
4
Y
2
9
5
N
3
9
2
M
3
9
4
I
3
9
5
[1]2bvj.a . . . . . . . . . . . . . . . . . . . . . * . . . . . . . . hem Fe
[1]2c7x.a . . . . . . . . . . . . . . * . . . . . . . . . . . . . . . hem Fe
[1]2cd8.b . . . . . . . . . . . . . . . . . . . * . . . . . . . . . . hem Fe
[1]2vz7.a . N . . . . . . . . . . . . . . . . . . . . . . . . . . . . hem Fe
[1]2vzm.a . N . . . . . . . . . . . . . . . . . . . . . . . . . . . . hem Fe
[1]2whw.b . N . . . . . . . * . . . . . . . . . . . . . . . . . . . . hem Fe
[1]2wi9.a . N . . . . . . . . * . . . . . . . . . . . . . . . . . . . hem Fe
[1]3zk5.b . N . . . . . . . . * . . . . . . . . . . . . . . . . . * . hem Fe
[1]3zpi.a . N . . . . . . . . . . . . . . . . . . . * . . . . . . . . hem Fe
[1]4b7d.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Fe
[1]4b7s.a . N . . . . . . . . . . . . . . . . . . . . . . . . . . . . hem Fe
[1]4umz.a . N . . . . . . . . . . . . . . . . . . . . . . . . . . . . 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
2bvj.a is apo
2c7x.a:nrb
2cd8.b:pxi
2vz7.a:pxi
2vzm.a:nrb
2whw.b:1d4
2wi9.a:1d2
3zk5.b:z18
3zpi.a is apo
4b7d.a:qle
4b7s.a:qle
4umz.a:xjo
[1] 2bvj.a
-
1.2 0.4 0.9 1.1 0.6 1.0 0.4 - 1.1 0.7 1.1
[1] 2c7x.a -
0
1.2 1.2 0.2 0.4 0.6 0.2 - 0.9 0.2 0.4
[1] 2cd8.b - 0.9
0.2
0.9 0.6 0.9 0.7 0 - 0.7 0.2 0.5
[1] 2vz7.a - 0.2 0.2
0.1
0.2 0.3 0.4 0 - 0.5 0 0.1
[1] 2vzm.a - 0.1 0 0.7
0.1
0.4 0.6 0 - 0.8 0 0.1
[1] 2whw.b - 1.4 1.4 3.0 0.9
0
0 0.6 - 0.4 0.3 0.2
[1] 2wi9.a - 1.8 1.1 1.9 1.1 0.1
0
0.4 - 0.2 0.5 0.8
[1] 3zk5.b - 1.3 0.8 1.6 1.1 0.5 0.6
0
- 1.0 0.1 0.3
[1] 3zpi.a - 1.4 0.4 0.8 1.1 0.1 0.3 0.1
-
0.4 0.4 0.8
[1] 4b7d.a - 1.3 0.6 1.5 1.0 0.1 0.1 0.1 -
0.1
0 0.1
[1] 4b7s.a - 0.5 0.3 1.2 0.4 0.9 0.6 0 - 0.7
0
0.2
[1] 4umz.a - 0.1 0.1 0.4 0.1 0.4 0.4 0 - 0.4 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
2bvj.a
2c7x.a
2cd8.b
2vz7.a
2vzm.a
2whw.b
2wi9.a
3zk5.b
3zpi.a
4b7d.a
4b7s.a
4umz.a
[1] 2bvj.a
0
.11 .06 .06 .07 .14 .12 .12 .05 .10 .09 .06
[1] 2c7x.a .11
0
.09 .06 .05 .15 .13 .11 .12 .11 .07 .05
[1] 2cd8.b .06 .09
0
.06 .06 .15 .12 .09 .06 .10 .05 .06
[1] 2vz7.a .06 .06 .06
0
.03 .11 .10 .08 .08 .08 .05 .02
[1] 2vzm.a .07 .05 .06 .03
0
.11 .10 .06 .09 .09 .04 .03
[1] 2whw.b .14 .15 .15 .11 .11
0
.13 .11 .13 .09 .12 .12
[1] 2wi9.a .12 .13 .12 .10 .10 .13
0
.10 .12 .08 .13 .09
[1] 3zk5.b .12 .11 .09 .08 .06 .11 .10
0
.10 .06 .06 .08
[1] 3zpi.a .05 .12 .06 .08 .09 .13 .12 .10
0
.08 .08 .07
[1] 4b7d.a .10 .11 .10 .08 .09 .09 .08 .06 .08
0
.07 .07
[1] 4b7s.a .09 .07 .05 .05 .04 .12 .13 .06 .08 .07
0
.05
[1] 4umz.a .06 .05 .06 .02 .03 .12 .09 .08 .07 .07 .05
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.2 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
2bvj.a
2c7x.a
2cd8.b
2vz7.a
2vzm.a
2whw.b
2wi9.a
3zk5.b
3zpi.a
4b7d.a
4b7s.a
4umz.a
[1] 2bvj.a
0
0.8 0.8 0.9 0.7 1.1 1.2 0.9 0.5 0.9 0.8 0.7
[1] 2c7x.a 0.8
0
0.7 0.9 0.5 1.4 1.2 0.8 0.9 1.1 0.5 0.8
[1] 2cd8.b 0.8 0.7
0
0.7 0.5 1.2 1.0 0.5 0.9 0.9 0.6 0.5
[1] 2vz7.a 0.9 0.9 0.7
0
0.7 1.1 0.9 0.7 1.0 1.0 0.9 0.6
[1] 2vzm.a 0.7 0.5 0.5 0.7
0
1.2 1.0 0.7 0.9 1.0 0.7 0.5
[1] 2whw.b 1.1 1.4 1.2 1.1 1.2
0
0.7 1.1 1.3 0.7 1.3 1.0
[1] 2wi9.a 1.2 1.2 1.0 0.9 1.0 0.7
0
0.9 1.3 0.9 1.1 0.9
[1] 3zk5.b 0.9 0.8 0.5 0.7 0.7 1.1 0.9
0
0.9 0.9 0.6 0.6
[1] 3zpi.a 0.5 0.9 0.9 1.0 0.9 1.3 1.3 0.9
0
1.0 0.8 0.8
[1] 4b7d.a 0.9 1.1 0.9 1.0 1.0 0.7 0.9 0.9 1.0
0
1.0 0.9
[1] 4b7s.a 0.8 0.5 0.6 0.9 0.7 1.3 1.1 0.6 0.8 1.0
0
0.8
[1] 4umz.a 0.7 0.8 0.5 0.6 0.5 1.0 0.9 0.6 0.8 0.9 0.8
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

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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
2bvj.a
2c7x.a
2cd8.b
2vz7.a
2vzm.a
2whw.b
2wi9.a
3zk5.b
3zpi.a
4b7d.a
4b7s.a
4umz.a
[1] 2bvj.a
0
1.2 1.0 1.2 1.2 1.4 1.2 1.3 0.8 1.3 1.1 1.0
[1] 2c7x.a 1.2
0
1.1 1.7 1.1 1.7 1.6 1.4 1.4 1.5 1.1 1.2
[1] 2cd8.b 1.0 1.1
0
1.2 0.9 1.4 1.1 0.9 0.9 1.1 1.1 0.9
[1] 2vz7.a 1.2 1.7 1.2
0
0.9 1.9 1.8 1.6 1.3 1.8 1.3 1.0
[1] 2vzm.a 1.2 1.1 0.9 0.9
0
1.8 1.7 1.4 1.1 1.6 0.9 0.7
[1] 2whw.b 1.4 1.7 1.4 1.9 1.8
0
1.1 1.3 1.8 1.1 1.8 1.7
[1] 2wi9.a 1.2 1.6 1.1 1.8 1.7 1.1
0
1.2 1.8 1.1 1.8 1.6
[1] 3zk5.b 1.3 1.4 0.9 1.6 1.4 1.3 1.2
0
1.4 1.0 1.4 1.3
[1] 3zpi.a 0.8 1.4 0.9 1.3 1.1 1.8 1.8 1.4
0
1.5 1.0 0.9
[1] 4b7d.a 1.3 1.5 1.1 1.8 1.6 1.1 1.1 1.0 1.5
0
1.5 1.4
[1] 4b7s.a 1.1 1.1 1.1 1.3 0.9 1.8 1.8 1.4 1.0 1.5
0
0.9
[1] 4umz.a 1.0 1.2 0.9 1.0 0.7 1.7 1.6 1.3 0.9 1.4 0.9
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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