SMTL ID : 4z0h.1

X-ray structure of cytoplasmic glyceraldehyde-3-phosphate dehydrogenase (GapC1) complexed with NAD

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

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, I.79, R.80, S.98, T.99, G.100, F.102, S.122, A.123, C.152, A.183, N.316, Y.320 Ligands: SO4.2 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:I.12, A:Y.320 Hydrogen bonds: A:F.9, A:R.11, A:I.12, A:R.80, A:N.316 Water bridges: A:G.10, A:A.183, A:A.183, A:E.317 pi-Stacking: A:F.35 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, I.36, R.80, S.98, T.99, G.100, S.122, A.123, C.152, A.183, N.316, E.317, Y.320 Ligands: SO4.6 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:N.316 Water bridges: B:E.317, B:E.317 pi-Stacking: B:F.35 NAD.10: 24 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.36, I.79, R.80, S.98, T.99, G.100, F.102, S.122, A.123, C.152, A.183, N.316, Y.320 Ligands: SO4.11 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:I.12, C:Y.320 Hydrogen bonds: C:F.9, C:R.11, C:I.12, C:R.80, C:N.316 Water bridges: C:G.10, C:A.183, C:A.183, C:E.317, C:E.317 pi-Stacking: C:F.35 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, I.36, R.80, S.98, T.99, G.100, S.122, A.123, C.152, A.183, N.316, E.317, Y.320 Ligands: SO4.15 12 PLIP interactions: 12 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:N.316 Water bridges: D:E.317 pi-Stacking: D:F.35

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 3 PLIP interactions: 3 interactions with chain A Water bridges: A:A.183, A:T.184 Salt bridges: A:R.234 SO4.3: 6 residues within 4Å: Chain A: P.124, S.151, T.153, T.211, G.212, A.213 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.151, A:T.153, A:T.211, A:T.211, A:G.212 SO4.4: 8 residues within 4Å: Chain A: S.203, P.236 Chain B: S.203 Chain C: S.203, P.236 Chain D: S.203, F.204 Ligands: SO4.13 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain D Hydrogen bonds: C:S.203, A:S.203, D:S.203 SO4.6: 4 residues within 4Å: Chain B: T.182, T.184, R.234 Ligands: NAD.5 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.182, B:T.182, B:T.184 Salt bridges: B:R.234 SO4.7: 6 residues within 4Å: Chain B: P.124, S.151, T.153, T.211, G.212, A.213 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.151, B:T.153, B:G.212, B:A.213 SO4.8: 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 SO4.9: 2 residues within 4Å: Chain B: K.271, R.291 2 PLIP interactions: 2 interactions with chain B Water bridges: B:S.266 Salt bridges: B:R.291 SO4.11: 4 residues within 4Å: Chain C: T.182, T.184, R.234 Ligands: NAD.10 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:T.182, C:T.184 Water bridges: C:A.183, C:T.184 Salt bridges: C:R.234 SO4.12: 6 residues within 4Å: Chain C: P.124, S.151, T.153, T.211, G.212, A.213 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.151, C:T.211, C:G.212 SO4.13: 8 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 Ligands: SO4.4 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: C:S.203, B:S.203, A:S.203 SO4.15: 4 residues within 4Å: Chain D: T.182, T.184, R.234 Ligands: NAD.14 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.182 Salt bridges: D:R.234 SO4.16: 6 residues within 4Å: Chain D: P.124, S.151, T.153, T.211, G.212, A.213 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:S.151, D:T.153, D:T.153, D:T.154, D:T.211, D:G.212, D:A.213 SO4.17: 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 SO4.18: 2 residues within 4Å: Chain D: K.271, R.291 2 PLIP interactions: 2 interactions with chain D Water bridges: D:S.266 Salt bridges: D:R.291

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zaffagnini, M. et al., Tuning Cysteine Reactivity and Sulfenic Acid Stability by Protein Microenvironment in Glyceraldehyde-3-Phosphate Dehydrogenases of Arabidopsis thaliana. Antioxid. Redox Signal. (2016)

Release Date

2016-04-13

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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