SMTL ID : 7zq3.1

Crystal structure of photosynthetic glyceraldehyde-3-phosphate dehydrogenase from Chlamydomonas reinhardtii (CrGAPA) complexed with NADP+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-tetramer

Ligands

4 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.1: 21 residues within 4Å: Chain A: G.18, F.19, G.20, R.21, I.22, N.44, S.46, S.89, R.90, G.108, T.109, G.110, V.111, F.112, T.132, A.133, C.164, N.327, Y.331 Chain B: S.203 Ligands: SO4.2 34 PLIP interactions: 27 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:I.22, A:Y.331 Hydrogen bonds: A:F.19, A:R.21, A:I.22, A:N.44, A:R.90, A:N.327, B:S.203, B:S.203 Water bridges: A:N.17, A:G.18, A:F.19, A:G.20, A:G.23, A:D.45, A:S.89, A:R.90, A:R.90, A:R.90, A:R.90, A:G.110, A:T.132, A:G.195, A:G.195, A:G.195, B:R.198, B:R.198, B:S.203, B:S.203, B:S.203 Salt bridges: A:R.90 pi-Cation interactions: A:R.90, A:R.90 NDP.6: 21 residues within 4Å: Chain A: S.203 Chain B: G.18, F.19, G.20, R.21, I.22, N.44, S.46, S.89, R.90, G.108, T.109, G.110, V.111, F.112, T.132, A.133, C.164, N.327, Y.331 Ligands: SO4.7 32 PLIP interactions: 26 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:I.22, B:Y.331 Hydrogen bonds: B:F.19, B:F.19, B:R.21, B:I.22, B:S.46, B:R.90, B:T.132, B:N.327, A:S.203, A:S.203 Water bridges: B:N.17, B:G.18, B:G.20, B:G.23, B:Q.51, B:R.90, B:R.90, B:R.90, B:G.110, B:T.132, B:G.195, B:G.195, B:G.195, A:R.198, A:S.203, A:S.203, A:S.203 Salt bridges: B:R.90 pi-Cation interactions: B:R.90, B:R.90 NDP.10: 21 residues within 4Å: Chain C: G.18, F.19, G.20, R.21, I.22, N.44, S.46, S.89, R.90, G.108, T.109, G.110, V.111, F.112, T.132, A.133, C.164, N.327, Y.331 Chain D: S.203 Ligands: SO4.11 34 PLIP interactions: 27 interactions with chain C, 7 interactions with chain D Hydrophobic interactions: C:I.22, C:Y.331 Hydrogen bonds: C:F.19, C:R.21, C:I.22, C:N.44, C:R.90, C:N.327, D:S.203, D:S.203 Water bridges: C:N.17, C:G.18, C:F.19, C:G.20, C:G.23, C:D.45, C:S.89, C:R.90, C:R.90, C:R.90, C:R.90, C:G.110, C:T.132, C:G.195, C:G.195, C:G.195, D:R.198, D:R.198, D:S.203, D:S.203, D:S.203 Salt bridges: C:R.90 pi-Cation interactions: C:R.90, C:R.90 NDP.15: 21 residues within 4Å: Chain C: S.203 Chain D: G.18, F.19, G.20, R.21, I.22, N.44, S.46, S.89, R.90, G.108, T.109, G.110, V.111, F.112, T.132, A.133, C.164, N.327, Y.331 Ligands: SO4.16 32 PLIP interactions: 26 interactions with chain D, 6 interactions with chain C Hydrophobic interactions: D:I.22, D:Y.331 Hydrogen bonds: D:F.19, D:F.19, D:R.21, D:I.22, D:S.46, D:R.90, D:T.132, D:N.327, C:S.203, C:S.203 Water bridges: D:N.17, D:G.18, D:G.20, D:G.23, D:Q.51, D:R.90, D:R.90, D:R.90, D:G.110, D:T.132, D:G.195, D:G.195, D:G.195, C:R.198, C:S.203, C:S.203, C:S.203 Salt bridges: D:R.90 pi-Cation interactions: D:R.90, D:R.90

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

SO4.2: 5 residues within 4Å: Chain A: T.194, D.196, R.209, R.245 Ligands: NDP.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.194, A:T.194 Water bridges: A:G.195, A:R.209, A:R.245 Salt bridges: A:R.209, A:R.245 SO4.3: 4 residues within 4Å: Chain A: S.163, T.222, G.223, A.224 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.163, A:G.223, A:A.224 Water bridges: A:S.163, A:C.164, A:T.165, A:T.166 SO4.4: 4 residues within 4Å: Chain A: E.267, N.270, R.274, A.308 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.270 Water bridges: A:R.274, A:R.274 Salt bridges: A:R.274 SO4.5: 1 residues within 4Å: Chain A: R.90 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.90 Salt bridges: A:R.90 SO4.7: 5 residues within 4Å: Chain B: T.194, D.196, R.209, R.245 Ligands: NDP.6 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.194 Water bridges: B:G.195, B:R.209, B:R.245 Salt bridges: B:R.209, B:R.245 SO4.8: 4 residues within 4Å: Chain B: S.163, T.222, G.223, A.224 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:S.163, B:T.222, B:T.222, B:G.223 Water bridges: B:R.245, B:R.245, B:R.245, B:R.245, B:R.245 SO4.9: 4 residues within 4Å: Chain B: E.267, N.270, R.274, A.308 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.270 Water bridges: B:E.267, B:R.274 Salt bridges: B:R.274 SO4.11: 5 residues within 4Å: Chain C: T.194, D.196, R.209, R.245 Ligands: NDP.10 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:T.194, C:T.194 Water bridges: C:G.195, C:R.209, C:R.245 Salt bridges: C:R.209, C:R.245 SO4.12: 4 residues within 4Å: Chain C: S.163, T.222, G.223, A.224 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:S.163, C:G.223, C:A.224 Water bridges: C:S.163, C:C.164, C:T.165, C:T.166 SO4.13: 4 residues within 4Å: Chain C: E.267, N.270, R.274, A.308 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.270 Water bridges: C:R.274, C:R.274 Salt bridges: C:R.274 SO4.14: 1 residues within 4Å: Chain C: R.90 2 PLIP interactions: 2 interactions with chain C Water bridges: C:R.90 Salt bridges: C:R.90 SO4.16: 5 residues within 4Å: Chain D: T.194, D.196, R.209, R.245 Ligands: NDP.15 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:T.194 Water bridges: D:G.195, D:R.209, D:R.245 Salt bridges: D:R.209, D:R.245 SO4.17: 4 residues within 4Å: Chain D: S.163, T.222, G.223, A.224 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:S.163, D:T.222, D:T.222, D:G.223 Water bridges: D:R.245, D:R.245, D:R.245, D:R.245, D:R.245 SO4.18: 4 residues within 4Å: Chain D: E.267, N.270, R.274, A.308 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:N.270 Water bridges: D:E.267, D:R.274 Salt bridges: D:R.274

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mattioli, E.J. et al., Structural snapshots of nitrosoglutathione binding and reactivity underlying S-nitrosylation of photosynthetic GAPDH. Redox Biol (2022)

Release Date

2022-07-20

Peptides

Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
O

B
R

C
O

D
R

Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic

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