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

Crystal structure of the photosynthetic A2B2-glyceraldehyde-3-phosphate dehydrogenase, complexed with NADP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.60 Å

Oligo State

hetero-2-2-mer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: T.185, D.187, R.200 Ligands: NDP.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.200 SO4.3: 6 residues within 4Å: Chain B: T.183, D.185, R.198, R.234 Ligands: SO4.4, NDP.5 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.183, B:T.183, B:R.234 Salt bridges: B:R.198 SO4.4: 7 residues within 4Å: Chain B: S.152, C.153, T.154, H.180, T.211, R.234 Ligands: SO4.3 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:S.152, B:C.153, B:T.154, B:T.154, B:T.211, B:T.211 Salt bridges: B:H.180, B:R.234 SO4.6: 6 residues within 4Å: Chain C: T.185, D.187, R.200, R.236, Y.367 Ligands: NDP.9 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.200, C:R.236, C:Y.367 SO4.7: 3 residues within 4Å: Chain C: G.143, H.144, K.337 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:H.144 Salt bridges: C:K.337 SO4.8: 1 residues within 4Å: Chain C: K.110 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:K.110 SO4.10: 5 residues within 4Å: Chain D: T.183, D.185, R.198 Ligands: SO4.11, NDP.13 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:T.183, D:D.185, D:D.185 Salt bridges: D:R.198, D:R.234 SO4.11: 6 residues within 4Å: Chain D: S.152, C.153, T.154, T.211, R.234 Ligands: SO4.10 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:S.152, D:T.154, D:T.154, D:T.211, D:T.211, D:G.212 Salt bridges: D:H.180, D:R.234 SO4.12: 3 residues within 4Å: Chain D: V.276, C.277, L.281 No protein-ligand interaction detected (PLIP)

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

NDP.2: 17 residues within 4Å: Chain A: G.8, F.9, G.10, R.11, I.12, N.34, R.80, G.98, T.99, G.100, T.122, A.123, C.155, N.319, E.320, Y.323 Ligands: SO4.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.323 Hydrogen bonds: A:F.9, A:F.9, A:G.10, A:I.12, A:R.80, A:R.80, A:N.319, A:E.320, A:E.320 NDP.5: 23 residues within 4Å: Chain B: N.7, G.8, G.10, R.11, I.12, N.34, D.35, T.36, D.79, R.80, G.98, T.99, G.100, F.102, T.122, A.123, C.153, T.183, N.316, E.317, Y.320 Chain C: E.368 Ligands: SO4.3 11 PLIP interactions: 11 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.34, B:T.36, B:R.80, B:T.122, B:N.316 NDP.9: 14 residues within 4Å: Chain C: F.9, G.10, R.11, I.12, R.80, G.98, T.99, G.100, T.122, C.155, T.185, N.319, E.320 Ligands: SO4.6 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:F.9, C:G.10, C:I.12, C:R.80, C:N.319, C:E.320 NDP.13: 18 residues within 4Å: Chain A: E.368 Chain D: G.10, R.11, I.12, D.35, T.36, D.79, R.80, G.98, T.99, G.100, T.122, A.123, C.153, T.183, N.316, Y.320 Ligands: SO4.10 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:I.12, D:I.12, D:Y.320 Hydrogen bonds: D:R.11, D:I.12, D:T.36, D:R.80, D:T.122, D:N.316

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fermani, S. et al., Molecular mechanism of thioredoxin regulation in photosynthetic A2B2-glyceraldehyde-3-phosphate dehydrogenase. Proc.Natl.Acad.Sci.Usa (2007)

Release Date

2007-06-19

Peptides

Glyceraldehyde-3-phosphate dehydrogenase B: AC
Glyceraldehyde-3-phosphate dehydrogenase A: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
O

C
Q

B
P

D
R

Glyceraldehyde-3-phosphate dehydrogenase B

Glyceraldehyde-3-phosphate dehydrogenase A

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