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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, 5y5f, 5y5g, 5y5h, 5y5i, 5y5j, 5y5k, 5y5l (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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