SMTL ID : 1rm5.2 (1 other biounit)

Crystal structure of mutant S188A of photosynthetic glyceraldehyde-3-phosphate dehydrogenase A4 isoform, complexed with NADP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: T.183, D.185, R.198, R.234 Ligands: NDP.4 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:T.183 Water bridges: A:G.184, A:D.185, A:D.185, A:D.185, A:R.234, A:R.234 Salt bridges: A:R.198, A:R.234 SO4.2: 4 residues within 4Å: Chain A: S.152, T.211, G.212, A.213 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.152, A:T.211, A:G.212, A:A.213 Water bridges: A:T.155 SO4.3: 3 residues within 4Å: Chain A: F.254, A.255, V.302 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.255, A:V.302 SO4.5: 5 residues within 4Å: Chain B: T.183, D.185, R.198, R.234 Ligands: NDP.8 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:T.183 Water bridges: B:G.184, B:D.185, B:D.185, B:D.185, B:R.234, B:R.234 Salt bridges: B:R.198, B:R.234 SO4.6: 4 residues within 4Å: Chain B: S.152, T.211, G.212, A.213 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.152, B:T.211, B:G.212, B:A.213 Water bridges: B:T.155 SO4.7: 3 residues within 4Å: Chain B: F.254, A.255, V.302 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.255, B:V.302 SO4.9: 5 residues within 4Å: Chain C: T.183, D.185, R.198, R.234 Ligands: NDP.12 7 PLIP interactions: 7 interactions with chain C Water bridges: C:G.184, C:D.185, C:D.185, C:R.234, C:R.234 Salt bridges: C:R.198, C:R.234 SO4.10: 4 residues within 4Å: Chain C: S.152, T.211, G.212, A.213 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:S.152, C:T.211, C:T.211, C:G.212, C:A.213 Water bridges: C:T.155, C:T.155 SO4.11: 3 residues within 4Å: Chain C: F.254, A.255, V.302 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:A.255, C:V.302 SO4.13: 5 residues within 4Å: Chain D: T.183, D.185, R.198, R.234 Ligands: NDP.16 7 PLIP interactions: 7 interactions with chain D Water bridges: D:G.184, D:D.185, D:D.185, D:R.234, D:R.234 Salt bridges: D:R.198, D:R.234 SO4.14: 4 residues within 4Å: Chain D: S.152, T.211, G.212, A.213 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:S.152, D:T.211, D:T.211, D:G.212, D:A.213 Water bridges: D:T.155, D:T.155 SO4.15: 3 residues within 4Å: Chain D: F.254, A.255, V.302 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:A.255, D:V.302

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

NDP.4: 18 residues within 4Å: Chain A: G.10, R.11, I.12, N.34, T.36, D.79, R.80, G.98, T.99, G.100, V.101, F.102, T.122, A.123, T.183, N.316, Y.320 Ligands: SO4.1 19 PLIP interactions: 18 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:I.12, A:Y.320 Hydrogen bonds: A:R.11, A:I.12, A:T.36, A:T.36, A:R.80, A:T.122, A:N.316 Water bridges: A:N.7, A:F.9, A:G.10, A:G.13, A:G.100, A:T.122, A:G.184, A:G.184, A:G.184, C:A.192 NDP.8: 18 residues within 4Å: Chain B: G.10, R.11, I.12, N.34, T.36, D.79, R.80, G.98, T.99, G.100, V.101, F.102, T.122, A.123, T.183, N.316, Y.320 Ligands: SO4.5 19 PLIP interactions: 18 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:I.12, B:Y.320 Hydrogen bonds: B:R.11, B:I.12, B:T.36, B:T.36, B:R.80, B:T.122, B:N.316 Water bridges: B:N.7, B:F.9, B:G.10, B:G.13, B:G.100, B:T.122, B:G.184, B:G.184, B:G.184, D:A.192 NDP.12: 18 residues within 4Å: Chain C: G.10, R.11, I.12, N.34, T.36, D.79, R.80, G.98, T.99, G.100, V.101, F.102, T.122, A.123, T.183, N.316, Y.320 Ligands: SO4.9 19 PLIP interactions: 18 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:I.12, C:Y.320 Hydrogen bonds: C:R.11, C:I.12, C:T.36, C:T.36, C:R.80, C:N.316 Water bridges: C:N.7, C:F.9, C:G.10, C:G.13, C:G.100, C:T.122, C:G.184, C:G.184, C:G.184, C:E.317, A:A.192 NDP.16: 18 residues within 4Å: Chain D: G.10, R.11, I.12, N.34, T.36, D.79, R.80, G.98, T.99, G.100, V.101, F.102, T.122, A.123, T.183, N.316, Y.320 Ligands: SO4.13 19 PLIP interactions: 18 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:I.12, D:Y.320 Hydrogen bonds: D:R.11, D:I.12, D:T.36, D:T.36, D:R.80, D:N.316 Water bridges: D:N.7, D:F.9, D:G.10, D:G.13, D:G.100, D:T.122, D:G.184, D:G.184, D:G.184, D:E.317, B:A.192

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sparla, F. et al., Coenzyme Site-directed Mutants of Photosynthetic A(4)-GAPDH Show Selectively Reduced NADPH-dependent Catalysis, Similar to Regulatory AB-GAPDH Inhibited by Oxidized Thioredoxin. J.Mol.Biol. (2004)

Release Date

2004-07-27

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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