SMTL ID : 6quq.1

Crystal structure of glutathionylated glycolytic glyceraldehyde-3- phosphate dehydrogenase from Arabidopsis thaliana (AtGAPC1)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.99 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 25 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.79, R.80, S.98, T.99, G.100, F.102, S.122, A.123, T.182, A.183, N.316, E.317, Y.320 Ligands: SO4.2, GSH.4 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:I.12, A:I.12, A:Y.320 Hydrogen bonds: A:N.7, A:F.9, A:R.11, A:I.12, A:N.32, A:D.33, A:R.80, A:N.316 NAD.6: 25 residues within 4Å: Chain A: P.191 Chain B: N.7, G.8, F.9, G.10, R.11, I.12, N.32, D.33, P.34, F.35, I.36, R.80, S.98, T.99, G.100, F.102, S.122, A.123, A.183, N.316, E.317, Y.320 Ligands: SO4.7, GSH.9 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:I.12, B:I.12, B:Y.320 Hydrogen bonds: B:F.9, B:R.11, B:I.12, B:N.32, B:R.80, B:S.122, B:N.316 Water bridges: B:A.183, B:E.317 NAD.12: 25 residues within 4Å: Chain C: N.7, G.8, F.9, G.10, R.11, I.12, N.32, D.33, P.34, F.35, I.79, R.80, S.98, T.99, G.100, F.102, S.122, A.123, T.182, A.183, N.316, E.317, Y.320 Ligands: SO4.13, GSH.15 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:I.12, C:I.12, C:Y.320 Hydrogen bonds: C:N.7, C:F.9, C:R.11, C:I.12, C:N.32, C:R.80, C:N.316 NAD.17: 25 residues within 4Å: Chain C: P.191 Chain D: N.7, G.8, F.9, G.10, R.11, I.12, N.32, D.33, P.34, F.35, I.36, R.80, S.98, T.99, G.100, F.102, S.122, A.123, A.183, N.316, E.317, Y.320 Ligands: SO4.18, GSH.20 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:I.12, D:I.12, D:Y.320 Hydrogen bonds: D:F.9, D:R.11, D:I.12, D:N.32, D:R.80, D:T.99, D:S.122, D:N.316 Water bridges: D:A.183, D:E.317

14 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 5 residues within 4Å: Chain A: T.182, T.184, R.234 Ligands: NAD.1, GSH.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.184 Salt bridges: A:R.234 SO4.3: 7 residues within 4Å: Chain A: P.124, S.151, T.153, T.211, G.212, A.213 Ligands: GSH.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.151, A:T.153, A:T.211, A:G.212, A:A.213 SO4.5: 9 residues within 4Å: Chain A: S.203, P.236 Chain B: S.203, F.204 Chain C: S.203, P.236 Chain D: S.203, F.204 Ligands: SO4.16 4 PLIP interactions: 1 interactions with chain A, 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: A:S.203, D:S.203, D:S.203, C:S.203 SO4.7: 5 residues within 4Å: Chain B: T.182, T.184, R.234 Ligands: NAD.6, GSH.9 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.182, B:T.182, B:T.184 Salt bridges: B:R.234 SO4.8: 8 residues within 4Å: Chain B: P.124, S.151, T.153, T.154, T.211, G.212, A.213 Ligands: GSH.9 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.151, B:S.151, B:G.212, B:A.213 SO4.10: 3 residues within 4Å: Chain B: G.288, N.290, W.318 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.290 SO4.11: 2 residues within 4Å: Chain B: K.271, R.291 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.272 Salt bridges: B:K.271, B:R.291 SO4.13: 5 residues within 4Å: Chain C: T.182, T.184, R.234 Ligands: NAD.12, GSH.15 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:T.182, C:T.184, C:T.184 Salt bridges: C:R.234 SO4.14: 7 residues within 4Å: Chain C: P.124, S.151, T.153, T.211, G.212, A.213 Ligands: GSH.15 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.151, C:G.212, C:A.213 SO4.16: 9 residues within 4Å: Chain A: S.203, P.236 Chain B: S.203, F.204 Chain C: S.203, P.236 Chain D: S.203, F.204 Ligands: SO4.5 4 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: B:S.203, B:S.203, C:S.203, A:S.203 SO4.18: 5 residues within 4Å: Chain D: T.182, T.184, R.234 Ligands: NAD.17, GSH.20 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.182 Salt bridges: D:R.234 SO4.19: 8 residues within 4Å: Chain D: P.124, S.151, T.153, T.154, T.211, G.212, A.213 Ligands: GSH.20 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:S.151, D:S.151, D:T.153, D:T.154, D:G.212, D:A.213 SO4.21: 3 residues within 4Å: Chain D: G.288, N.290, W.318 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.290 SO4.22: 2 residues within 4Å: Chain D: K.271, R.291 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:G.272 Salt bridges: D:K.271, D:R.291

4 x GSH: GLUTATHIONE(Non-covalent)

GSH.4: 17 residues within 4Å: Chain A: S.122, A.123, P.124, A.150, S.151, C.152, T.153, T.177, H.179, S.209, S.210, T.211, S.232, R.234 Ligands: NAD.1, SO4.2, SO4.3 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:P.124, A:T.153, A:S.210, A:T.211, A:T.211, A:S.232, A:R.234 Salt bridges: A:H.179, A:R.234 GSH.9: 15 residues within 4Å: Chain B: A.123, P.124, A.150, S.151, C.152, H.179, S.209, S.210, T.211, S.232, R.234, N.316 Ligands: NAD.6, SO4.7, SO4.8 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:C.152, B:S.209, B:S.210, B:S.210, B:S.232, B:R.234 Salt bridges: B:H.179, B:R.234 GSH.15: 17 residues within 4Å: Chain C: S.122, A.123, P.124, A.150, S.151, C.152, T.153, T.177, H.179, S.209, S.210, T.211, S.232, R.234 Ligands: NAD.12, SO4.13, SO4.14 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:P.124, C:S.210, C:T.211, C:T.211, C:S.232, C:R.234, C:Y.314 Salt bridges: C:H.179, C:R.234 GSH.20: 15 residues within 4Å: Chain D: A.123, P.124, A.150, S.151, C.152, H.179, S.209, S.210, T.211, S.232, R.234, N.316 Ligands: NAD.17, SO4.18, SO4.19 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:C.152, D:S.209, D:S.210, D:S.210, D:S.232, D:R.234 Salt bridges: D:H.179, D:R.234

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zaffagnini, M. et al., Glutathionylation primes soluble glyceraldehyde-3-phosphate dehydrogenase for late collapse into insoluble aggregates. Proc.Natl.Acad.Sci.USA (2019)

Release Date

2019-12-04

Peptides

Glyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
O

B
R

C
O

D
R

Glyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic

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