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CINA_CITBR_7_404

1,8-cineole 2-endo-monooxygenase [Cytochrome P450 family]

Composition of the binding site

Protein chains monomer
A1 (CINA_CITBR):76, 77, 81, 88, 91, 234, 237:239, 242, 285:287, 385, 38676, 77, 81, 88, 91, 234, 237:239, 242, 285:287, 385, 386
Cofactors (cF):hem
Metals (Me):Fe

Full PDB list

1t2b, 3bdz, 3be0, 4fb2, 4fmx, 4fyz, 4l6g, 4l77, 4lht (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 cF Me
V
7
6
T
7
7
Y
8
1
L
8
8
A
9
1
I
2
3
4
L
2
3
7
G
2
3
8
N
2
4
2
A
2
8
5
V
2
8
7
V
3
8
6
[1]3bdz.a mli7 . . . . . . . . A . . . hem Fe
[1]4fb2.a none . . . . . . . . . . . . hem Fe
[1]4fmx.a cnl11 . . . . . . . . . . . . hem Fe
[1]4l6g.a cnl11 . . F . . . . . . . . . hem Fe
[1]4l77.a cnl11 . . . . . . . . A . . . 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
V
7
6
T
7
7
Y
8
1
L
8
8
A
9
1
I
2
3
4
L
2
3
7
G
2
3
8
G
2
3
9
N
2
4
2
A
2
8
5
M
2
8
6
V
2
8
7
Q
3
8
5
V
3
8
6
[1]3bdz.a . . . . . . . . . A . . . . . hem Fe
[1]4fb2.a . . . . . . . . . . . . . . . hem Fe
[1]4fmx.a . . . . . . . . . . . . . . . hem Fe
[1]4l6g.a . . F . . . . . . . . . . . . hem Fe
[1]4l77.a . . . . . . . . . A . . . . . 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
3bdz.a:mli
4fb2.a is apo
4fmx.a:cnl
4l6g.a:cnl
4l77.a:cnl
[1] 3bdz.a
0
- 0 0 0
[1] 4fb2.a 0.6
-
0.5 0.5 0.4
[1] 4fmx.a 0.2 -
0
0 0.1
[1] 4l6g.a 0.1 - 0
0
0
[1] 4l77.a 0 - 0 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
3bdz.a
4fb2.a
4fmx.a
4l6g.a
4l77.a
[1] 3bdz.a
0
.04 .02 .01 0
[1] 4fb2.a .04
0
.05 .03 .04
[1] 4fmx.a .02 .05
0
.01 .02
[1] 4l6g.a .01 .03 .01
0
.01
[1] 4l77.a 0 .04 .02 .01
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.7 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
3bdz.a
4fb2.a
4fmx.a
4l6g.a
4l77.a
[1] 3bdz.a
0
1.9 0.7 0.8 0.3
[1] 4fb2.a 1.9
0
2.1 2.1 1.9
[1] 4fmx.a 0.7 2.1
0
0.2 0.8
[1] 4l6g.a 0.8 2.1 0.2
0
0.8
[1] 4l77.a 0.3 1.9 0.8 0.8
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.8 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
3bdz.a
4fb2.a
4fmx.a
4l6g.a
4l77.a
[1] 3bdz.a
0
3.7 0.8 0.8 0.5
[1] 4fb2.a 3.7
0
3.7 3.4 3.6
[1] 4fmx.a 0.8 3.7
0
0.3 0.7
[1] 4l6g.a 0.8 3.4 0.3
0
0.7
[1] 4l77.a 0.5 3.6 0.7 0.7
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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