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T4HR_MAGO7_1_283

Tetrahydroxynaphthalene reductase [Short-chain dehydrogenases/reductases (SDR) family]

Composition of the binding site

Protein chains monomer
A1 (T4HR_MAGO7):118, 164:166, 178, 209, 210, 215, 216, 219, 220, 223, 243, 283118, 164:166, 178, 209, 210, 215, 216, 219, 220, 223, 243, 283
Cofactors (cF):ndp

Full PDB list

1doh, 1g0n, 1g0o, 1ybv

Pocket contact map

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PDB.ch
   
ligand
A1 cF
S
1
6
4
I
1
6
5
T
1
6
6
Y
1
7
8
G
2
0
9
G
2
1
0
M
2
1
5
Y
2
1
6
V
2
1
9
C
2
2
0
Y
2
2
3
W
2
4
3
M
2
8
3
[1]1doh.a nid13 . . . . . . . . . . . . . ndp
[1]1g0n.a phh14 . . . . . . . . . . . . . ndp
[1]1g0n.b none . . . . . . . . - - - . . ndp
[1]1g0o.a pyq13 . . . . . . . . . . . . . ndp
[1]1ybv.a bea13 . . . . . . . . . . . . . ndp

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

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PDB.ch
A1 cF
V
1
1
8
S
1
6
4
I
1
6
5
T
1
6
6
Y
1
7
8
G
2
0
9
G
2
1
0
M
2
1
5
Y
2
1
6
V
2
1
9
C
2
2
0
Y
2
2
3
W
2
4
3
M
2
8
3
[1]1doh.a . . . . . . . . . . . . . . ndp
[1]1g0n.a . . . . . . . . . . . . . . ndp
[1]1g0n.b . . . . . . . . . - - - . . ndp
[1]1g0o.a . . . . . . . . . . . . . . ndp
[1]1ybv.a . . . . . . . . . . . . . . ndp

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
1doh.a:nid
1g0n.a:phh
1g0n.b is apo
1g0o.a:pyq
1ybv.a:bea
[1] 1doh.a
0
0.7 - 0 0.2
[1] 1g0n.a 0
0.3
- 0 0.1
[1] 1g0n.b 0 0.4
-
0 0.1
[1] 1g0o.a 0 0.3 -
0
0.2
[1] 1ybv.a 0 0.2 - 0
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
1doh.a
1g0n.a
1g0n.b
1g0o.a
1ybv.a
[1] 1doh.a
0
.03 .04 .03 .04
[1] 1g0n.a .03
0
.01 0 .02
[1] 1g0n.b .04 .01
0
.01 .03
[1] 1g0o.a .03 0 .01
0
.02
[1] 1ybv.a .04 .02 .03 .02
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.5 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
1doh.a
1g0n.a
1g0n.b
1g0o.a
1ybv.a
[1] 1doh.a
0
0.3 0.3 0.2 0.5
[1] 1g0n.a 0.3
0
0.1 0.2 0.6
[1] 1g0n.b 0.3 0.1
0
0.3 0.6
[1] 1g0o.a 0.2 0.2 0.3
0
0.5
[1] 1ybv.a 0.5 0.6 0.6 0.5
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
1doh.a
1g0n.a
1g0n.b
1g0o.a
1ybv.a
[1] 1doh.a
0
0.3 0.4 0.5 0.8
[1] 1g0n.a 0.3
0
0.2 0.5 0.8
[1] 1g0n.b 0.4 0.2
0
0.5 0.8
[1] 1g0o.a 0.5 0.5 0.5
0
0.7
[1] 1ybv.a 0.8 0.8 0.8 0.7
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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