SMTL ID : 6lgm.1

Crystal structure of an oxido-reductase with mutation and inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

3 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 27 residues within 4Å: Chain A: N.7, G.8, F.9, G.10, R.11, I.12, N.32, D.33, P.34, F.35, I.36, E.77, R.78, S.96, T.97, G.98, F.100, S.120, A.121, S.150, A.181, N.314, E.315, Y.318 Chain C: P.189 Ligands: PO4.2, 9HB.3 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:I.12, A:Y.318 Hydrogen bonds: A:F.9, A:F.9, A:R.11, A:I.12, A:R.78, A:N.314 Water bridges: A:N.7, A:N.7, A:G.10, A:G.98, A:S.120, A:A.181, A:A.181 pi-Stacking: A:F.35 NAD.4: 26 residues within 4Å: Chain B: N.7, G.8, F.9, G.10, R.11, I.12, N.32, D.33, P.34, F.35, I.36, E.77, R.78, S.96, T.97, G.98, F.100, S.120, A.121, S.150, A.181, N.314, Y.318 Chain D: P.189 Ligands: PO4.5, 9HB.6 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:I.12, B:Y.318 Hydrogen bonds: B:N.7, B:F.9, B:F.9, B:R.11, B:I.12, B:N.32, B:R.78, B:S.150, B:S.150 Water bridges: B:G.10, B:G.13, B:G.98, B:S.120, B:A.181, B:A.181 pi-Stacking: B:F.35 NAD.7: 27 residues within 4Å: Chain A: P.189 Chain C: N.7, G.8, F.9, G.10, R.11, I.12, N.32, D.33, P.34, F.35, I.36, E.77, R.78, S.96, T.97, G.98, F.100, S.120, A.121, S.150, A.181, N.314, E.315, Y.318 Ligands: PO4.8, 9HB.9 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:I.12, C:Y.318 Hydrogen bonds: C:N.7, C:F.9, C:R.11, C:I.12, C:N.32, C:R.78, C:N.314 Water bridges: C:G.10, C:G.13, C:G.98, C:S.120 pi-Stacking: C:F.35

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 5 residues within 4Å: Chain A: T.180, T.182, R.232 Ligands: NAD.1, 9HB.3 2 PLIP interactions: 2 interactions with chain A Water bridges: A:A.181 Salt bridges: A:R.232 PO4.5: 5 residues within 4Å: Chain B: T.180, T.182, R.232 Ligands: NAD.4, 9HB.6 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.180, B:T.182 Salt bridges: B:R.232 PO4.8: 5 residues within 4Å: Chain C: T.180, T.182, R.232 Ligands: NAD.7, 9HB.9 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.180, C:T.182 Salt bridges: C:R.232 PO4.10: 6 residues within 4Å: Chain D: S.149, T.151, T.152, T.209, G.210, A.211 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:S.149, D:S.149, D:T.152, D:G.210 Water bridges: D:S.150, D:T.151

3 x 9HB: Dimethyl fumarate(Non-covalent)

9HB.3: 11 residues within 4Å: Chain A: P.122, S.149, S.150, T.151, T.152, H.177, T.209, G.210, A.211 Ligands: NAD.1, PO4.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.150, A:T.151, A:T.151, A:T.209, A:G.210, A:A.211 Salt bridges: A:H.177 9HB.6: 9 residues within 4Å: Chain B: S.149, S.150, T.151, H.177, T.209, G.210, A.211 Ligands: NAD.4, PO4.5 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.149, B:S.150, B:T.151 Salt bridges: B:H.177 9HB.9: 9 residues within 4Å: Chain C: S.149, S.150, T.151, H.177, T.209, G.210, A.211 Ligands: NAD.7, PO4.8 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.149 Salt bridges: C:H.177

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, Y. et al., Crystal structure of an oxido-reductase with mutation and inhibitor. To Be Published

Release Date

2020-12-09

Peptides

Glyceraldehyde-3-phosphate dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Glyceraldehyde-3-phosphate dehydrogenase

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