SMTL ID : 6yne.1

GAPDH purified from the supernatant of HEK293F cells: crystal form 2 of 4.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-tetramer

Ligands

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

XPE.1: 8 residues within 4Å: Chain A: H.165, D.166, N.167, F.168, G.169, E.250, K.251, P.252 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.251 XPE.2: 9 residues within 4Å: Chain A: D.127, A.128, P.129, M.130, F.131, N.136, K.139, L.144, K.219 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.130 XPE.3: 9 residues within 4Å: Chain A: A.183, T.184, Q.185, K.186, P.191, S.192, G.193 Chain D: Q.185, K.186 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.186 XPE.4: 11 residues within 4Å: Chain A: G.298, A.299, G.300, I.301 Chain C: L.195, R.197, P.208, A.209, S.210, M.231, A.232 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:G.298, C:R.197 Water bridges: C:R.197 XPE.5: 10 residues within 4Å: Chain B: D.127, A.128, P.129, M.130, F.131, N.136, K.139, L.144, K.219, V.220 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:M.130 Water bridges: B:N.136 XPE.6: 13 residues within 4Å: Chain B: L.195, R.197, P.208, A.209, S.210, T.211, M.231, A.232 Chain D: Q.280, G.298, A.299, G.300, I.301 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.197, B:S.210 Water bridges: B:R.197 XPE.7: 11 residues within 4Å: Chain B: Q.280, G.298, A.299, G.300, I.301 Chain D: L.195, R.197, P.208, A.209, S.210, M.231 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:G.300, D:R.197 XPE.8: 13 residues within 4Å: Chain A: L.195, W.196, R.197, P.208, A.209, S.210, T.211, M.231 Chain C: Q.280, G.298, A.299, G.300, I.301 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:R.197, A:S.210 Water bridges: A:S.210, C:A.302 XPE.9: 10 residues within 4Å: Chain C: D.127, A.128, P.129, M.130, F.131, N.136, K.139, L.144, K.219, V.220 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:M.130 XPE.10: 8 residues within 4Å: Chain B: A.183, T.184, Q.185, K.186 Chain C: A.183, T.184, Q.185, K.186 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:K.186, B:K.186 XPE.11: 7 residues within 4Å: Chain D: H.165, D.166, N.167, F.168, G.169, E.250, K.251 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.251 XPE.12: 8 residues within 4Å: Chain B: V.171, E.172, R.248 Chain D: V.171, R.248, L.249, E.250, H.306 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:R.248, D:R.248 Water bridges: B:R.248 XPE.13: 11 residues within 4Å: Chain D: M.105, D.127, A.128, P.129, M.130, F.131, N.136, K.139, L.144, K.219, V.220 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:M.130 Water bridges: D:N.136

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
A

B
B

C
C

D
D

Glyceraldehyde-3-phosphate dehydrogenase

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