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AZOR1_PSEAE_1_212

FMN-dependent NADH-azoreductase 1 [Azoreductase type 1 family]

Composition of the binding site

Protein chains homodimer
A1 (AZOR1_PSEAE):12, 99, 100, 147:149, 151, 157, 160, 187, 18812, 99, 100, 147:149, 151, 157, 160, 187, 188
A2 (AZOR1_PSEAE):56, 60, 114, 120, 131, 17356, 60, 114, 120, 131, 173
Cofactors (cF):fmn

Full PDB list

2v9c, 3keg, 3lt5, 3r6w, 4n65, 4n9q

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 A2 cF
R
1
2
N
9
9
F
1
0
0
G
1
4
7
G
1
4
8
H
1
4
9
F
1
5
1
N
1
5
7
E
1
8
8
V
5
6
F
6
0
V
1
1
4
F
1
2
0
Y
1
3
1
F
1
7
3
[1]2v9c.a mre20 . . . . . . . . - . . . . . . fmn
[1]3keg.b mre20 . . . . . . . . . . . . . F . fmn
[1]3lt5.a blq19 . . . . . . . . . . . . . . . fmn
[1]3r6w.a nfz14 . . . . . . . . . . . . . . . fmn
[1]4n65.a none . . . . . . . . . . . . . . . fmn
[1]4n65.b aqn20 . . . . . . . . - . . . . . . fmn
[1]4n9q.b uq118 . . . . . . . . - . . . . . . fmn

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 A2 cF
R
1
2
N
9
9
F
1
0
0
G
1
4
7
G
1
4
8
H
1
4
9
F
1
5
1
N
1
5
7
M
1
6
0
E
1
8
7
E
1
8
8
V
5
6
F
6
0
V
1
1
4
F
1
2
0
Y
1
3
1
F
1
7
3
[1]2v9c.a . . . . . . . . . - - . . . . . . fmn
[1]3keg.b . . . . . . . . . * * . . . . F . fmn
[1]3lt5.a . . . . . . . . . * * . . . . . . fmn
[1]3r6w.a . . . . . . . . . * * . . . . . . fmn
[1]4n65.a . . . . . . . . . * * . . . . . . fmn
[1]4n65.b . . . . . . . . . - - . . . . . . fmn
[1]4n9q.b . . . . . . . . . * - . . . . . . fmn

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
2v9c.a:mre
3keg.b:mre
3lt5.a:blq
3r6w.a:nfz
4n65.a is apo
4n65.b:aqn
4n9q.b:uq1
[1] 2v9c.a
0
0.2 0.1 0 - 0 0.2
[1] 3keg.b 2.0
0
0.1 0.1 - 0.9 0.2
[1] 3lt5.a 3.6 2.0
0
0 - 2.9 1.8
[1] 3r6w.a 3.6 2.1 0.2
0.1
- 3.0 1.4
[1] 4n65.a 3.6 1.8 0.1 0.1
-
2.7 1.1
[1] 4n65.b 0 0 0 0 -
0.1
0.1
[1] 4n9q.b 0.9 0.1 0 0 - 0.1
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
2v9c.a
3keg.b
3lt5.a
3r6w.a
4n65.a
4n65.b
4n9q.b
[1] 2v9c.a
0
.14 .23 .22 .22 .03 .07
[1] 3keg.b .14
0
.14 .14 .14 .12 .08
[1] 3lt5.a .23 .14
0
.01 .01 .22 .21
[1] 3r6w.a .22 .14 .01
0
0 .23 .21
[1] 4n65.a .22 .14 .01 0
0
.23 .21
[1] 4n65.b .03 .12 .22 .23 .23
0
.06
[1] 4n9q.b .07 .08 .21 .21 .21 .06
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
2v9c.a
3keg.b
3lt5.a
3r6w.a
4n65.a
4n65.b
4n9q.b
[1] 2v9c.a
0
0.2 0.2 0.2 0.2 0.4 0.3
[1] 3keg.b 0.2
0
0.5 0.6 0.6 0.5 0.5
[1] 3lt5.a 0.2 0.5
0
0.2 0.2 0.5 0.6
[1] 3r6w.a 0.2 0.6 0.2
0
0.2 0.5 0.5
[1] 4n65.a 0.2 0.6 0.2 0.2
0
0.5 0.6
[1] 4n65.b 0.4 0.5 0.5 0.5 0.5
0
0.2
[1] 4n9q.b 0.3 0.5 0.6 0.5 0.6 0.2
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

zoom: [−] [+]; [view as image]; [download as text]

pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
2v9c.a
3keg.b
3lt5.a
3r6w.a
4n65.a
4n65.b
4n9q.b
[1] 2v9c.a
0
0.9 1.0 0.4 1.1 0.9 0.8
[1] 3keg.b 0.9
0
1.4 1.6 1.5 0.9 0.9
[1] 3lt5.a 1.0 1.4
0
0.9 0.8 0.9 0.9
[1] 3r6w.a 0.4 1.6 0.9
0
1.1 0.9 0.9
[1] 4n65.a 1.1 1.5 0.8 1.1
0
0.5 0.6
[1] 4n65.b 0.9 0.9 0.9 0.9 0.5
0
0.2
[1] 4n9q.b 0.8 0.9 0.9 0.9 0.6 0.2
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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