SMTL ID : 1nbo.1 (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

8 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.3 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.183 Water bridges: A:G.184, A:D.185, A:R.198, A:R.198 Salt bridges: A:R.198, A:R.234 SO4.2: 7 residues within 4Å: Chain A: S.152, C.153, T.154, H.180, T.211, R.234 Ligands: SO4.1 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.152, A:C.153, A:T.154, A:T.154, A:T.211, A:T.211, A:R.234 Salt bridges: A:H.180 SO4.4: 6 residues within 4Å: Chain B: T.183, D.185, R.198, R.234 Ligands: SO4.5, NAD.6 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:T.183 Water bridges: B:G.184, B:D.185, B:R.198, B:R.198 Salt bridges: B:R.198, B:R.234 SO4.5: 7 residues within 4Å: Chain B: S.152, C.153, T.154, H.180, T.211, R.234 Ligands: SO4.4 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, B:R.234 Salt bridges: B:H.180 SO4.7: 6 residues within 4Å: Chain C: T.183, D.185, R.198, R.234 Ligands: SO4.8, NAD.9 6 PLIP interactions: 6 interactions with chain C Water bridges: C:G.184, C:D.185, C:R.198, C:R.198 Salt bridges: C:R.198, C:R.234 SO4.8: 7 residues within 4Å: Chain C: S.152, C.153, T.154, H.180, T.211, R.234 Ligands: SO4.7 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:S.152, C:C.153, C:T.154, C:T.154, C:T.211, C:T.211, C:R.234 Salt bridges: C:H.180 SO4.10: 6 residues within 4Å: Chain D: T.183, D.185, R.198, R.234 Ligands: SO4.11, NAD.12 6 PLIP interactions: 6 interactions with chain D Water bridges: D:G.184, D:D.185, D:R.198, D:R.198 Salt bridges: D:R.198, D:R.234 SO4.11: 7 residues within 4Å: Chain D: S.152, C.153, T.154, H.180, T.211, R.234 Ligands: SO4.10 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:S.152, D:C.153, D:T.154, D:T.154, D:T.211, D:T.211, D:R.234 Salt bridges: D:H.180

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

NAD.3: 21 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, N.316, E.317, Y.320 Ligands: SO4.1 19 PLIP interactions: 17 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:I.12, A:Y.320 Hydrogen bonds: A:F.9, A:R.11, A:I.12, A:T.36, A:R.80, A:T.122, A:N.316, C:S.192, C:S.192 Water bridges: A:N.7, A:G.10, A:G.13, A:R.14, A:G.100, A:G.184, A:G.184, A:G.184 NAD.6: 21 residues within 4Å: Chain B: 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, N.316, E.317, Y.320 Ligands: SO4.4 19 PLIP interactions: 17 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: B:I.12, B:Y.320 Hydrogen bonds: B:F.9, B:R.11, B:I.12, B:T.36, B:R.80, B:T.122, B:N.316, D:S.192, D:S.192 Water bridges: B:N.7, B:G.10, B:G.13, B:R.14, B:G.100, B:G.184, B:G.184, B:G.184 NAD.9: 21 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, N.316, E.317, Y.320 Ligands: SO4.7 20 PLIP interactions: 18 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:I.12, C:Y.320 Hydrogen bonds: C:F.9, C:R.11, C:I.12, C:T.36, C:R.80, C:N.316, A:S.192, A:S.192 Water bridges: C:N.7, C:G.10, C:G.13, C:R.14, C:G.100, C:G.184, C:G.184, C:G.184, C:E.317, C:E.317 NAD.12: 21 residues within 4Å: Chain D: 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, N.316, E.317, Y.320 Ligands: SO4.10 20 PLIP interactions: 18 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: D:I.12, D:Y.320 Hydrogen bonds: D:F.9, D:R.11, D:I.12, D:T.36, D:R.80, D:N.316, B:S.192, B:S.192 Water bridges: D:N.7, D:G.10, D:G.13, D:R.14, D:G.100, D:G.184, D:G.184, D:G.184, D:E.317, D:E.317

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
O

B
O

C
O

D
O

glyceraldehyde-3-phosphate dehydrogenase A

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