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DLDH_MYCTU_1_464

Dihydrolipoyl dehydrogenase [Class-I pyridine nucleotide-disulfide oxidoreductase family]

Composition of the binding site

Protein chains homodimer
A1 (DLDH_MYCTU):13, 16, 41, 42, 93, 96, 97, 99, 100, 317, 32113, 16, 41, 42, 93, 96, 97, 99, 100, 317, 321
A2 (DLDH_MYCTU):381, 383, 443, 448, 463, 464381, 383, 443, 448, 463, 464
Cofactors (cF):fad

Full PDB list

2a8x, 3ii4, 4m52 (redundant Pocketome entry)

Pocket contact map

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PDB.ch
   
ligand
A1 A2 cF
P
1
3
Y
1
6
C
4
1
L
4
2
R
9
3
G
9
6
V
9
7
F
9
9
L
1
0
0
E
3
2
1
A
3
8
1
A
3
8
3
H
4
4
3
E
4
4
8
N
4
6
3
[1]2a8x.a none . . . . . . . . . . . . . . . fad
[1]4m52.c m5225 . . . . . . . . . . . . . . . fad

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 A2 cF
P
1
3
Y
1
6
C
4
1
L
4
2
R
9
3
G
9
6
V
9
7
F
9
9
L
1
0
0
A
3
1
7
E
3
2
1
A
3
8
1
A
3
8
3
H
4
4
3
E
4
4
8
N
4
6
3
F
4
6
4
[1]2a8x.a . . . . * . . . . . . . . . . . . fad
[1]4m52.c . . . . . . . . . . . . . . . . . fad

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
2a8x.a is apo
4m52.c:m52
[1] 2a8x.a
-
3.7
[1] 4m52.c -
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
2a8x.a
4m52.c
[1] 2a8x.a
0
.21
[1] 4m52.c .21
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.8 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
2a8x.a
4m52.c
[1] 2a8x.a
0
0.5
[1] 4m52.c 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
2a8x.a
4m52.c
[1] 2a8x.a
0
1.7
[1] 4m52.c 1.7
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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