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CP126_MYCTU_1_414

Putative cytochrome P450 126 [Cytochrome P450 family]

Composition of the binding site

Protein chains monomer
A1 (CP126_MYCTU):13, 46, 80, 81, 83:86, 88, 90, 94, 96, 97, 189:192, 245, 246, 248:250, 252:254, 257, 300, 302:304, 399:40113, 46, 80, 81, 83:86, 88, 90, 94, 96, 97, 189:192, 245, 246, 248:250, 252:254, 257, 300, 302:304, 399:401
Cofactors (cF):hem
Metals (Me):Fe

Full PDB list

5li6, 5li7, 5li8, 5lie

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 cF Me
T
1
3
P
4
6
V
8
4
L
8
8
V
9
0
V
9
4
N
9
6
M
9
7
L
2
4
5
F
2
4
6
H
2
4
8
L
2
4
9
L
2
5
0
S
2
5
2
A
2
5
3
G
2
5
4
T
2
5
7
S
3
0
0
S
3
0
2
K
3
0
3
R
3
0
4
N
3
9
9
R
4
0
0
H
4
0
1
[1]5li6.a 6xf30 . . . . . . . . . . . . . . . . . . . . . . . . hem Fe
[1]5li7.b 6xd22 . . . . . . . . . . . . . . . . . . . . . . . . hem Fe
[1]5li8.a kkk36 . . . . . . . . . . . . . . . . . . . . . . . . hem Fe
[2]5lie.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

[download in TSV format]
   
PDB.ch
A1 cF Me
T
1
3
P
4
6
F
8
0
G
8
1
T
8
3
V
8
4
L
8
5
Q
8
6
L
8
8
V
9
0
V
9
4
N
9
6
M
9
7
T
1
8
9
M
1
9
0
P
1
9
1
R
1
9
2
L
2
4
5
F
2
4
6
H
2
4
8
L
2
4
9
L
2
5
0
S
2
5
2
A
2
5
3
G
2
5
4
T
2
5
7
S
3
0
0
S
3
0
2
K
3
0
3
R
3
0
4
N
3
9
9
R
4
0
0
H
4
0
1
[1]5li6.a . . . . . * * . . . . . . - - - - . . . * . . . . . . . . . . . . hem Fe
[1]5li7.b . . . . . * * . . . . . . - - - - . . . * . . . . . . . . . . . . hem Fe
[1]5li8.a . . * . . . . . . . . . . - - - - . . . * . . . . . . . . . . . . hem Fe
[2]5lie.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
5li6.a:6xf
5li7.b:6xd
5li8.a:kkk
5lie.b is apo
[1] 5li6.a
0
0.4 5.3 -
[1] 5li7.b 0.7
0
6.0 -
[1] 5li8.a 3.9 3.0
0
-
[2] 5lie.b 7.1 6.5 9.8
-
[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
5li6.a
5li7.b
5li8.a
5lie.b
[1] 5li6.a
0
.03 .24 .36
[1] 5li7.b .03
0
.24 .34
[1] 5li8.a .24 .24
0
.58
[2] 5lie.b .36 .34 .58
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.3 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
5li6.a
5li7.b
5li8.a
5lie.b
[1] 5li6.a
0
1.0 7.7 0.6
[1] 5li7.b 1.0
0
7.7 1.0
[1] 5li8.a 7.7 7.7
0
7.7
[2] 5lie.b 0.6 1.0 7.7
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 1.0 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
5li6.a
5li7.b
5li8.a
5lie.b
[1] 5li6.a
0
1.1 7.7 1.2
[1] 5li7.b 1.1
0
7.7 1.4
[1] 5li8.a 7.7 7.7
0
7.8
[2] 5lie.b 1.2 1.4 7.8
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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