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PLDH_RHILO_2_248

Pyridoxal 4-dehydrogenase [Short-chain dehydrogenases/reductases (SDR) family]

Composition of the binding site

Protein chains monomer
A1 (PLDH_RHILO):92, 141:143, 151, 154, 186, 197, 24592, 141:143, 151, 154, 186, 197, 245
Cofactors (cF):nad

Full PDB list

3ndr, 3nug, 3rwb

Pocket contact map

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PDB.ch
   
ligand
A1 cF
V
9
2
S
1
4
1
N
1
4
2
T
1
4
3
M
1
5
1
Y
1
5
4
L
1
8
6
H
1
9
7
M
2
4
5
[1]3ndr.a none . . . . * . . . * nad
[1]3nug.a none . . . . . . . . . nad
[1]3rwb.a 4pl12 . . . . . . . . . nad

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
9
2
S
1
4
1
N
1
4
2
T
1
4
3
M
1
5
1
Y
1
5
4
L
1
8
6
H
1
9
7
M
2
4
5
[1]3ndr.a . . . . * . . . * nad
[1]3nug.a . . . . . . . . . nad
[1]3rwb.a . . . . . . . . . nad

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
3ndr.a is apo
3nug.a is apo
3rwb.a:4pl
[1] 3ndr.a
-
- 0.2
[1] 3nug.a -
-
0.2
[1] 3rwb.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
3ndr.a
3nug.a
3rwb.a
[1] 3ndr.a
0
0 .01
[1] 3nug.a 0
0
.01
[1] 3rwb.a .01 .01
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.2 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
3ndr.a
3nug.a
3rwb.a
[1] 3ndr.a
0
0.2 0.2
[1] 3nug.a 0.2
0
0.1
[1] 3rwb.a 0.2 0.1
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.1 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
3ndr.a
3nug.a
3rwb.a
[1] 3ndr.a
0
0.6 0.6
[1] 3nug.a 0.6
0
0.2
[1] 3rwb.a 0.6 0.2
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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