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

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

14 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.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.198, A:R.234 Water bridges: A:D.185, A:R.198 SO4.2: 5 residues within 4Å: Chain A: S.152, T.154, T.211, G.212, A.213 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.152, A:T.211, A:T.211, A:G.212, A:A.213 SO4.3: 3 residues within 4Å: Chain A: E.256, N.259, R.263 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.263 SO4.4: 3 residues within 4Å: Chain A: G.38, V.39, K.40 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.39, A:K.40 Water bridges: A:Q.41 SO4.6: 5 residues within 4Å: Chain B: T.183, D.185, R.198, R.234 Ligands: NDP.9 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.183, B:D.185 Salt bridges: B:R.198, B:R.234 SO4.7: 5 residues within 4Å: Chain B: S.152, T.154, T.211, G.212, A.213 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.152, B:T.154, B:T.211, B:G.212, B:A.213 Water bridges: B:T.155, B:R.234 SO4.8: 3 residues within 4Å: Chain B: S.250, K.251, K.252 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.252 SO4.10: 5 residues within 4Å: Chain C: T.183, D.185, R.198, R.234 Ligands: NDP.14 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.198, C:R.234 Water bridges: C:D.185, C:R.198 SO4.11: 5 residues within 4Å: Chain C: S.152, T.154, T.211, G.212, A.213 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:S.152, C:T.211, C:T.211, C:G.212, C:A.213 SO4.12: 3 residues within 4Å: Chain C: E.256, N.259, R.263 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.263 SO4.13: 3 residues within 4Å: Chain C: G.38, V.39, K.40 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:V.39, C:K.40 Water bridges: C:Q.41 SO4.15: 5 residues within 4Å: Chain D: T.183, D.185, R.198, R.234 Ligands: NDP.18 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:T.183, D:D.185 Salt bridges: D:R.198, D:R.234 SO4.16: 5 residues within 4Å: Chain D: S.152, T.154, T.211, G.212, A.213 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:S.152, D:T.154, D:T.211, D:G.212, D:A.213 Water bridges: D:T.155, D:R.234 SO4.17: 3 residues within 4Å: Chain D: S.250, K.251, K.252 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.252

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

NDP.5: 16 residues within 4Å: Chain A: G.10, R.11, I.12, N.34, T.36, R.80, G.98, T.99, G.100, F.102, T.122, A.123, N.316, Y.320 Chain B: A.192 Ligands: SO4.1 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:I.12, A:I.12, A:Y.320 Hydrogen bonds: A:R.11, A:I.12, A:R.80, A:N.316 Water bridges: A:N.7, A:G.10, A:G.13, A:N.34, A:T.99, A:G.100, A:G.184, A:G.184, A:G.184, A:G.184, A:G.184, A:E.317 NDP.9: 15 residues within 4Å: Chain B: G.10, R.11, I.12, N.34, T.36, R.80, G.98, T.99, G.100, F.102, T.122, A.123, N.316, Y.320 Ligands: SO4.6 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:I.12, B:Y.320 Hydrogen bonds: B:R.11, B:I.12, B:N.34, B:T.36, B:T.36, B:R.80, B:T.122, B:N.316 Water bridges: B:F.9, B:F.9, B:G.10, B:G.13, B:G.100, B:G.184, B:G.184, B:G.184, B:G.184 NDP.14: 16 residues within 4Å: Chain C: G.10, R.11, I.12, N.34, T.36, R.80, G.98, T.99, G.100, F.102, T.122, A.123, N.316, Y.320 Chain D: A.192 Ligands: SO4.10 19 PLIP interactions: 19 interactions with chain C Hydrophobic interactions: C:I.12, C:I.12, C:Y.320 Hydrogen bonds: C:R.11, C:I.12, C:R.80, C:N.316 Water bridges: C:N.7, C:G.10, C:G.13, C:N.34, C:T.99, C:G.100, C:G.184, C:G.184, C:G.184, C:G.184, C:G.184, C:E.317 NDP.18: 15 residues within 4Å: Chain D: G.10, R.11, I.12, N.34, T.36, R.80, G.98, T.99, G.100, F.102, T.122, A.123, N.316, Y.320 Ligands: SO4.15 19 PLIP interactions: 19 interactions with chain D Hydrophobic interactions: D:I.12, D:Y.320 Hydrogen bonds: D:R.11, D:I.12, D:N.34, D:T.36, D:T.36, D:R.80, D:T.122, D:N.316 Water bridges: D:F.9, D:F.9, D:G.10, D:G.13, D:G.100, D:G.184, D:G.184, D:G.184, D:G.184

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
A

B
B

C
A

D
B

Glyceraldehyde 3-phosphate dehydrogenase A

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