SMTL ID : 6ynd.2 (1 other biounit)

GAPDH purified from the supernatant of HEK293F cells: crystal form 1 of 4.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.52 Å

Oligo State

homo-tetramer

Ligands

8 x XPE: 3,6,9,12,15,18,21,24,27-NONAOXANONACOSANE-1,29-DIOL(Non-covalent)

XPE.1: 11 residues within 4Å: Chain A: D.127, A.128, P.129, M.130, F.131, N.136, K.139, Y.140, L.144, K.219, V.220 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.130 XPE.2: 7 residues within 4Å: Chain A: H.165, D.166, N.167, F.168, G.169, E.250, K.251 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.251 XPE.3: 11 residues within 4Å: Chain B: D.127, A.128, P.129, M.130, F.131, N.136, K.139, Y.140, L.144, K.219, V.220 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:M.130 XPE.4: 7 residues within 4Å: Chain B: H.165, D.166, N.167, F.168, G.169, E.250, K.251 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.251 XPE.5: 11 residues within 4Å: Chain C: A.128, P.129, M.130, F.131, N.136, K.139, Y.140, D.141, L.144, K.219, V.220 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:M.130 XPE.6: 7 residues within 4Å: Chain C: H.165, D.166, N.167, F.168, G.169, E.250, K.251 No protein-ligand interaction detected (PLIP) XPE.7: 11 residues within 4Å: Chain D: D.127, A.128, P.129, M.130, F.131, N.136, K.139, Y.140, L.144, K.219, V.220 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:M.130 XPE.8: 7 residues within 4Å: Chain D: H.165, D.166, N.167, F.168, G.169, E.250, K.251 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.251 Water bridges: D:E.250

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lia, A. et al., Partial catalytic Cys oxidation of human GAPDH to Cys-sulfonic acid. Wellcome Open Res (2020)

Release Date

2020-05-06

Peptides

Glyceraldehyde-3-phosphate dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

C
F

D
G

Glyceraldehyde-3-phosphate dehydrogenase

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