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NOR_FUSOX_1_403

NADP nitrous oxide-forming nitric oxide reductase [Cytochrome P450 family]

Composition of the binding site

Protein chains monomer
A1 (NOR_FUSOX):64, 73, 75, 76, 78, 79, 87, 88, 174, 175, 184, 188, 235, 238:240, 243, 286, 28964, 73, 75, 76, 78, 79, 87, 88, 174, 175, 184, 188, 235, 238:240, 243, 286, 289
Cofactors (cF):hem
Metals (Me):Fe

Full PDB list

1cl6, 1cmj, 1cmn, 1ehe, 1ehf, 1ehg, 1f24, 1f25, 1f26, 1ged, 1gei, 1gej, 1jfb, 1jfc, 1rom, 1ulw, 1xqd, 2rom (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 cF Me
R
6
4
S
7
5
G
7
6
Q
7
8
A
7
9
V
8
7
R
1
7
4
T
1
7
5
A
1
8
4
N
1
8
8
L
2
3
5
A
2
3
9
G
2
4
0
T
2
4
3
S
2
8
6
A
2
8
9
[1]1cl6.a none . . . . . . . . . . . . . . . . hem Fe
[1]1cmn.a none . . . . . . . . . . . . . . V . hem Fe
[1]1ehf.a none . . . . . . . . . . . . . . T . hem Fe
[1]1f24.a none . . . . . . . . . . . . . A . . hem Fe
[1]1f25.a none . . . . . . . . . . . . . N . . hem Fe
[1]1f26.a none . . . . . . . . . . . . . V . . hem Fe
[1]1ulw.a none . G . . . . . . . . . . . . . . hem Fe
[1]1xqd.a dnd44 . G . . . . . . . . . . . . . . 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
R
6
4
S
7
3
S
7
5
G
7
6
Q
7
8
A
7
9
V
8
7
D
8
8
R
1
7
4
T
1
7
5
A
1
8
4
N
1
8
8
L
2
3
5
V
2
3
8
A
2
3
9
G
2
4
0
T
2
4
3
S
2
8
6
A
2
8
9
[1]1cl6.a . . . . . . . . . . . . . . . . . . . hem Fe
[1]1cmn.a . . . . . . . . . . . . . . . . . V . hem Fe
[1]1ehf.a . . . . . . . . . . . . . . . . . T . hem Fe
[1]1f24.a . . . . . . . . . . . . . . . . A . . hem Fe
[1]1f25.a . . . . . . . . . . . . . . . . N . . hem Fe
[1]1f26.a . . . . . . . . . . . . . . . . V . . hem Fe
[1]1ulw.a . G G . . . . . . . . . . . . . . . . hem Fe
[1]1xqd.a . G G . . . . . . . . . . . . . . . . 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
1cl6.a is apo
1cmn.a is apo
1ehf.a is apo
1f24.a is apo
1f25.a is apo
1f26.a is apo
1ulw.a is apo
1xqd.a:dnd
[1] 1cl6.a
-
- - - - - - 1.0
[1] 1cmn.a -
-
- - - - - 1.1
[1] 1ehf.a - -
-
- - - - 1.3
[1] 1f24.a - - -
-
- - - 1.1
[1] 1f25.a - - - -
-
- - 1.6
[1] 1f26.a - - - - -
-
- 1.1
[1] 1ulw.a - - - - - -
-
0.5
[1] 1xqd.a - - - - - - -
0.1
[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
1cl6.a
1cmn.a
1ehf.a
1f24.a
1f25.a
1f26.a
1ulw.a
1xqd.a
[1] 1cl6.a
0
.03 .03 .02 .04 .02 .03 .05
[1] 1cmn.a .03
0
.01 .01 .04 .01 .04 .06
[1] 1ehf.a .03 .01
0
.02 .04 .01 .04 .06
[1] 1f24.a .02 .01 .02
0
.04 .01 .04 .06
[1] 1f25.a .04 .04 .04 .04
0
.03 .06 .08
[1] 1f26.a .02 .01 .01 .01 .03
0
.03 .05
[1] 1ulw.a .03 .04 .04 .04 .06 .03
0
.02
[1] 1xqd.a .05 .06 .06 .06 .08 .05 .02
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.9 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
1cl6.a
1cmn.a
1ehf.a
1f24.a
1f25.a
1f26.a
1ulw.a
1xqd.a
[1] 1cl6.a
0
0.3 0.3 0.2 0.2 0.2 0.6 2.3
[1] 1cmn.a 0.3
0
0.2 0.3 0.2 0.2 0.5 2.3
[1] 1ehf.a 0.3 0.2
0
0.2 0.2 0.2 0.5 2.3
[1] 1f24.a 0.2 0.3 0.2
0
0.2 0.2 0.6 2.3
[1] 1f25.a 0.2 0.2 0.2 0.2
0
0.2 0.6 2.3
[1] 1f26.a 0.2 0.2 0.2 0.2 0.2
0
0.6 2.3
[1] 1ulw.a 0.6 0.5 0.5 0.6 0.6 0.6
0
2.3
[1] 1xqd.a 2.3 2.3 2.3 2.3 2.3 2.3 2.3
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.3 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
1cl6.a
1cmn.a
1ehf.a
1f24.a
1f25.a
1f26.a
1ulw.a
1xqd.a
[1] 1cl6.a
0
0.7 0.6 0.4 0.9 0.9 0.9 2.4
[1] 1cmn.a 0.7
0
0.8 0.7 0.9 0.9 0.7 2.5
[1] 1ehf.a 0.6 0.8
0
0.6 0.9 1.0 0.9 2.5
[1] 1f24.a 0.4 0.7 0.6
0
0.9 0.9 0.9 2.4
[1] 1f25.a 0.9 0.9 0.9 0.9
0
0.4 0.8 2.4
[1] 1f26.a 0.9 0.9 1.0 0.9 0.4
0
0.9 2.4
[1] 1ulw.a 0.9 0.7 0.9 0.9 0.8 0.9
0
2.4
[1] 1xqd.a 2.4 2.5 2.5 2.4 2.4 2.4 2.4
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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