SMTL ID : 6lgj.1

Crystal structure of an oxido-reductase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 22 residues within 4Å: Chain A: N.7, G.8, G.10, R.11, I.12, N.32, D.33, P.34, F.35, E.77, R.78, S.96, T.97, G.98, F.100, S.120, A.121, C.150, A.181, N.314, Y.318 Chain D: P.189 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:I.12, A:Y.318 Hydrogen bonds: A:N.7, A:R.11, A:I.12, A:N.32, A:E.77, A:N.314 Water bridges: A:G.10, A:G.13, A:T.180, A:T.180 pi-Stacking: A:F.35 NAD.2: 24 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, C.150, A.181, N.314, Y.318 Chain C: P.189 16 PLIP interactions: 15 interactions with chain B, 1 interactions with chain C 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:R.78, B:N.314 Water bridges: B:G.10, B:G.13, B:R.14, B:N.32, B:N.32, C:D.187 pi-Stacking: B:F.35 NAD.3: 24 residues within 4Å: Chain B: 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, C.150, A.181, N.314, Y.318 16 PLIP interactions: 15 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:I.12, C:Y.318 Hydrogen bonds: C:N.7, C:F.9, C:F.9, C:R.11, C:I.12, C:N.32, C:R.78 Water bridges: C:G.10, C:G.13, C:R.14, C:A.181, C:A.181, B:D.187 pi-Stacking: C:F.35 NAD.4: 19 residues within 4Å: Chain A: P.189 Chain D: G.8, G.10, R.11, I.12, D.33, P.34, F.35, R.78, S.96, T.97, G.98, F.100, S.120, A.121, C.150, A.181, N.314, Y.318 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:I.12, D:Y.318 Hydrogen bonds: D:R.11, D:I.12, D:R.78, D:N.314 Water bridges: D:G.10, D:G.98, D:G.98 pi-Stacking: D:F.35

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, Y. et al., Crystal structure of an oxido-reductase. 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