SMTL ID : 6qun.1

Crystal structure of AtGapC1 with the catalytic Cys149 irreversibly oxidized by H2O2 treatment

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 23 residues within 4Å: Chain A: N.7, G.8, F.9, G.10, R.11, I.12, N.32, D.33, P.34, I.36, R.80, S.98, T.99, G.100, F.102, S.122, A.123, C.152, A.183, N.316, E.317, Y.320 Ligands: SO4.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.12, A:Y.320 Hydrogen bonds: A:R.11, A:I.12, A:N.32, A:R.80, A:G.100, A:N.316 NAD.5: 23 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, R.80, S.98, T.99, G.100, F.102, S.122, A.123, C.152, A.183, N.316, E.317, Y.320 Ligands: SO4.6 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:I.12, B:Y.320 Hydrogen bonds: B:R.11, B:I.12, B:N.32, B:R.80, B:N.316 NAD.10: 23 residues within 4Å: Chain C: N.7, G.8, F.9, G.10, R.11, I.12, N.32, D.33, P.34, I.36, R.80, S.98, T.99, G.100, F.102, S.122, A.123, C.152, A.183, N.316, E.317, Y.320 Ligands: SO4.11 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:I.12, C:Y.320 Hydrogen bonds: C:R.11, C:I.12, C:N.32, C:R.80, C:G.100, C:N.316 NAD.14: 23 residues within 4Å: Chain D: N.7, G.8, F.9, G.10, R.11, I.12, N.32, D.33, P.34, F.35, R.80, S.98, T.99, G.100, F.102, S.122, A.123, C.152, A.183, N.316, E.317, Y.320 Ligands: SO4.15 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:I.12, D:Y.320 Hydrogen bonds: D:R.11, D:I.12, D:N.32, D:R.80, D:T.99, D:N.316

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

SO4.2: 4 residues within 4Å: Chain A: T.182, T.184, R.234 Ligands: NAD.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.184 Salt bridges: A:R.234 SO4.3: 6 residues within 4Å: Chain A: S.151, C.152, T.153, T.211, G.212, A.213 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.151, A:T.153, A:T.211, A:T.211, A:G.212, A:A.213 SO4.4: 9 residues within 4Å: Chain A: S.203 Chain B: S.203, F.204 Chain C: S.203, P.236 Chain D: S.203, F.204, P.236 Ligands: SO4.13 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:P.236, C:S.203, C:S.203 SO4.6: 4 residues within 4Å: Chain B: T.182, T.184, R.234 Ligands: NAD.5 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.182, B:T.184 Salt bridges: B:R.234 SO4.7: 5 residues within 4Å: Chain B: S.151, T.153, T.211, G.212, A.213 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.151, B:T.153, B:T.153, B:T.211, B:G.212, B:A.213 SO4.8: 2 residues within 4Å: Chain B: N.290, W.318 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.290 SO4.9: 2 residues within 4Å: Chain B: K.271, R.291 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.271, B:R.291 SO4.11: 4 residues within 4Å: Chain C: T.182, T.184, R.234 Ligands: NAD.10 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:T.182, C:T.184, C:T.184 Salt bridges: C:R.234 SO4.12: 6 residues within 4Å: Chain C: S.151, C.152, T.153, T.211, G.212, A.213 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.151, C:T.211, C:G.212, C:A.213 SO4.13: 9 residues within 4Å: Chain A: S.203, P.236 Chain B: S.203, F.204, P.236 Chain C: S.203 Chain D: S.203, F.204 Ligands: SO4.4 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:S.203, A:S.203, D:P.236 SO4.15: 4 residues within 4Å: Chain D: T.182, T.184, R.234 Ligands: NAD.14 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:R.234 SO4.16: 5 residues within 4Å: Chain D: S.151, T.153, T.211, G.212, A.213 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:S.151, D:T.153, D:T.153, D:G.212, D:A.213 SO4.17: 2 residues within 4Å: Chain D: N.290, W.318 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.290 SO4.18: 2 residues within 4Å: Chain D: K.271, R.291 2 PLIP interactions: 2 interactions with chain D Salt bridges: D:K.271, D:R.291

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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