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

The dual coenzyme specificity of photosynthetic glyceraldehyde-3-phosphate dehydrogenase interpreted by the crystal structure of A4 isoform complexed with NAD

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 6 residues within 4Å: Chain A: T.183, D.185, R.198, R.234 Ligands: SO4.2, NAD.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.183 Water bridges: A:G.184 Salt bridges: A:R.198, A:R.234 SO4.2: 5 residues within 4Å: Chain A: S.152, T.154, T.211, A.213 Ligands: SO4.1 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: 4 residues within 4Å: Chain A: D.79, R.80, N.81, N.84 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.80, A:N.81, A:N.81 Salt bridges: A:R.80 SO4.5: 6 residues within 4Å: Chain B: T.183, D.185, R.198, R.234 Ligands: SO4.6, NAD.8 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.183 Salt bridges: B:R.198, B:R.234 SO4.6: 6 residues within 4Å: Chain B: S.152, T.154, T.211, G.212, A.213 Ligands: SO4.5 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.152, B:T.154, B:T.154, B:G.212, B:A.213 Water bridges: B:R.234, B:R.234 SO4.7: 3 residues within 4Å: Chain B: F.254, A.255, V.302 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.255, B:V.302, B:V.302 SO4.9: 6 residues within 4Å: Chain C: T.183, D.185, R.198, R.234 Ligands: SO4.10, NAD.12 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:T.183 Water bridges: C:G.184 Salt bridges: C:R.198, C:R.234 SO4.10: 5 residues within 4Å: Chain C: S.152, T.154, T.211, A.213 Ligands: SO4.9 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 SO4.11: 4 residues within 4Å: Chain C: D.79, R.80, N.81, N.84 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.80, C:N.81, C:N.81 Salt bridges: C:R.80 SO4.13: 6 residues within 4Å: Chain D: T.183, D.185, R.198, R.234 Ligands: SO4.14, NAD.16 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:T.183 Salt bridges: D:R.198, D:R.234 SO4.14: 6 residues within 4Å: Chain D: S.152, T.154, T.211, G.212, A.213 Ligands: SO4.13 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:S.152, D:T.154, D:T.154, D:G.212, D:A.213 Water bridges: D:R.234, D:R.234 SO4.15: 3 residues within 4Å: Chain D: F.254, A.255, V.302 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:A.255, D:V.302, D:V.302

4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.4: 22 residues within 4Å: Chain A: G.8, F.9, 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 Ligands: SO4.1 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:I.12, A:Y.320 Hydrogen bonds: A:F.9, A:R.11, A:I.12, A:R.80, A:N.316, A:N.316 Water bridges: A:G.10, A:G.13, A:N.34, A:G.100, A:T.122, A:G.184, A:G.184 NAD.8: 18 residues within 4Å: Chain B: G.8, G.10, R.11, I.12, N.34, D.35, T.36, R.80, G.98, T.99, G.100, F.102, T.122, A.123, C.153, N.316, Y.320 Ligands: SO4.5 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.12, B:Y.320 Hydrogen bonds: B:R.11, B:I.12, B:N.34, B:T.36, B:R.80, B:T.122, B:N.316, A:S.192 Water bridges: B:G.100, B:G.100 NAD.12: 22 residues within 4Å: Chain C: G.8, F.9, 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 Ligands: SO4.9 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:I.12, C:Y.320 Hydrogen bonds: C:F.9, C:R.11, C:I.12, C:R.80, C:N.316, C:N.316 Water bridges: C:G.10, C:G.13, C:N.34, C:G.100, C:T.122, C:G.184, C:G.184 NAD.16: 18 residues within 4Å: Chain D: G.8, G.10, R.11, I.12, N.34, D.35, T.36, R.80, G.98, T.99, G.100, F.102, T.122, A.123, C.153, N.316, Y.320 Ligands: SO4.13 12 PLIP interactions: 11 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:I.12, D:Y.320 Hydrogen bonds: D:R.11, D:I.12, D:N.34, D:T.36, D:R.80, D:T.122, D:N.316, C:S.192 Water bridges: D:G.100, D:G.100

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Falini, G. et al., Dual Coenzyme Specificity of Photosynthetic Glyceraldehyde-3-phosphate Dehydrogenase Interpreted by the Crystal Structure of A(4) Isoform Complexed with NAD. Biochemistry (2003)

Release Date

2003-05-13

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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