SMTL ID : 1jn0.2 (1 other biounit)

Crystal structure of the non-regulatory A4 isoform of spinach chloroplast glyceraldehyde-3-phosphate dehydrogenase complexed with NADP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: T.181, D.183, R.196, R.232 Ligands: NDP.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.181, A:D.183 Salt bridges: A:R.196, A:R.232 SO4.2: 6 residues within 4Å: Chain A: S.150, T.152, S.208, T.209, G.210, A.211 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.150, A:S.150, A:T.152, A:S.208, A:G.210, A:A.211 SO4.4: 5 residues within 4Å: Chain B: T.181, D.183, R.196, R.232 Ligands: NDP.6 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.181, B:D.183 Salt bridges: B:R.196, B:R.232 SO4.5: 6 residues within 4Å: Chain B: S.150, T.152, S.208, T.209, G.210, A.211 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.150, B:S.150, B:T.152, B:S.208, B:G.210, B:A.211 SO4.7: 5 residues within 4Å: Chain C: T.181, D.183, R.196, R.232 Ligands: NDP.9 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.183 Salt bridges: C:R.196, C:R.232 SO4.8: 6 residues within 4Å: Chain C: S.150, T.152, S.208, T.209, G.210, A.211 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:S.150, C:S.150, C:T.152, C:S.208, C:T.209, C:G.210, C:A.211 SO4.10: 5 residues within 4Å: Chain D: T.181, D.183, R.196, R.232 Ligands: NDP.12 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:D.183 Salt bridges: D:R.196, D:R.232 SO4.11: 6 residues within 4Å: Chain D: S.150, T.152, S.208, T.209, G.210, A.211 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:S.150, D:S.150, D:T.152, D:S.208, D:T.209, D:G.210, D:A.211

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

NDP.3: 20 residues within 4Å: Chain A: G.8, G.10, R.11, I.12, N.33, T.35, D.77, R.78, G.96, T.97, G.98, F.100, T.120, A.121, C.151, N.314, E.315, Y.318 Chain C: S.190 Ligands: SO4.1 16 PLIP interactions: 15 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:I.12, A:Y.318 Hydrogen bonds: A:R.11, A:I.12, A:N.33, A:T.35, A:T.35, A:T.35, A:R.78, A:N.314, C:S.190 Water bridges: A:G.10, A:G.13, A:T.181, A:G.182, A:E.315 NDP.6: 20 residues within 4Å: Chain B: G.8, G.10, R.11, I.12, N.33, T.35, D.77, R.78, G.96, T.97, G.98, F.100, T.120, A.121, C.151, N.314, E.315, Y.318 Chain D: S.190 Ligands: SO4.4 16 PLIP interactions: 15 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:I.12, B:Y.318 Hydrogen bonds: B:R.11, B:I.12, B:N.33, B:T.35, B:T.35, B:T.35, B:R.78, B:N.314, D:S.190 Water bridges: B:G.10, B:G.13, B:T.181, B:G.182, B:E.315 NDP.9: 20 residues within 4Å: Chain A: S.190 Chain C: G.8, G.10, R.11, I.12, N.33, T.35, D.77, R.78, G.96, T.97, G.98, F.100, T.120, A.121, C.151, N.314, E.315, Y.318 Ligands: SO4.7 16 PLIP interactions: 15 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:I.12, C:Y.318 Hydrogen bonds: C:R.11, C:I.12, C:N.33, C:T.35, C:T.35, C:R.78, C:N.314, A:S.190 Water bridges: C:G.10, C:G.13, C:T.181, C:G.182, C:E.315, C:E.315 NDP.12: 20 residues within 4Å: Chain B: S.190 Chain D: G.8, G.10, R.11, I.12, N.33, T.35, D.77, R.78, G.96, T.97, G.98, F.100, T.120, A.121, C.151, N.314, E.315, Y.318 Ligands: SO4.10 16 PLIP interactions: 15 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:I.12, D:Y.318 Hydrogen bonds: D:R.11, D:I.12, D:N.33, D:T.35, D:T.35, D:R.78, D:N.314, B:S.190 Water bridges: D:G.10, D:G.13, D:T.181, D:G.182, D:E.315, D:E.315

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fermani, S. et al., Crystal structure of the non-regulatory A(4 )isoform of spinach chloroplast glyceraldehyde-3-phosphate dehydrogenase complexed with NADP. J.Mol.Biol. (2001)

Release Date

2001-11-30

Peptides

GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE A: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
O

B
O

C
O

D
O

GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE A

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