SMTL ID : 7u5m.1

Cryo-EM Structure of GAPDH

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

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

NAD.1: 24 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, C.150, A.181, N.314, E.315, Y.318 Chain C: P.189 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:I.12, A:Y.318 Hydrogen bonds: A:R.11, A:I.12, A:R.78, A:N.314 Water bridges: A:F.9, A:R.14, A:A.181 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, C.150, A.181, N.314, E.315, Y.318 Chain D: P.189 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:I.12, B:Y.318 Hydrogen bonds: B:R.11, B:I.12, B:R.78, B:N.314 Water bridges: B:F.9, B:R.14, B:A.181 NAD.3: 24 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, C.150, A.181, N.314, E.315, Y.318 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:I.12, C:Y.318 Hydrogen bonds: C:R.11, C:I.12, C:R.78, C:N.314 Water bridges: C:F.9, C:R.14 NAD.4: 24 residues within 4Å: Chain B: P.189 Chain D: 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, C.150, A.181, N.314, E.315, 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:F.9, D:G.10, D:R.14, D:A.181

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Morgan, C.E. et al., Toward structural-omics of the bovine retinal pigment epithelium. Cell Rep (2022)

Release Date

2022-12-14

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