SMTL ID : 3k2b.3 (2 other biounits)

Crystal structure of photosynthetic A4 isoform glyceraldehyde-3-phosphate dehydrogenase complexed with NAD, from Arabidopsis thaliana

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 22 residues within 4Å: Chain A: G.9, F.10, G.11, R.12, I.13, N.35, D.36, T.37, R.81, G.99, T.100, G.101, V.102, F.103, T.123, A.124, C.154, T.184, N.317, E.318, Y.321 Ligands: SO4.2 17 PLIP interactions: 2 interactions with chain C, 15 interactions with chain A Hydrogen bonds: C:S.193, C:S.193, A:F.10, A:R.12, A:I.13, A:T.37, A:R.81, A:R.81, A:N.317 Hydrophobic interactions: A:I.13, A:Y.321 Water bridges: A:N.8, A:G.11, A:G.14, A:R.81, A:G.101, A:G.185 NAD.8: 22 residues within 4Å: Chain B: G.9, F.10, G.11, R.12, I.13, N.35, D.36, T.37, N.80, R.81, G.99, T.100, G.101, V.102, F.103, T.123, A.124, C.154, T.184, N.317, Y.321 Ligands: SO4.9 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:I.13, B:Y.321 Hydrogen bonds: B:F.10, B:R.12, B:I.13, B:T.37, B:R.81, B:T.123, B:N.317 Water bridges: B:G.101, B:T.123 NAD.14: 22 residues within 4Å: Chain C: G.9, F.10, G.11, R.12, I.13, N.35, D.36, T.37, R.81, G.99, T.100, G.101, V.102, F.103, T.123, A.124, C.154, T.184, N.317, E.318, Y.321 Ligands: SO4.15 17 PLIP interactions: 15 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:I.13, C:Y.321 Hydrogen bonds: C:F.10, C:R.12, C:I.13, C:T.37, C:R.81, C:R.81, C:N.317, A:S.193, A:S.193 Water bridges: C:N.8, C:G.11, C:G.14, C:R.81, C:G.101, C:G.185 NAD.21: 22 residues within 4Å: Chain D: G.9, F.10, G.11, R.12, I.13, N.35, D.36, T.37, N.80, R.81, G.99, T.100, G.101, V.102, F.103, T.123, A.124, C.154, T.184, N.317, Y.321 Ligands: SO4.22 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:I.13, D:Y.321 Hydrogen bonds: D:F.10, D:R.12, D:I.13, D:T.37, D:R.81, D:T.123, D:N.317 Water bridges: D:G.101, D:T.123

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

SO4.2: 5 residues within 4Å: Chain A: T.184, D.186, R.199, R.235 Ligands: NAD.1 Ligand excluded by PLIP SO4.3: 5 residues within 4Å: Chain A: S.153, T.155, T.212, G.213, A.214 Ligand excluded by PLIP SO4.4: 3 residues within 4Å: Chain A: G.64, E.65, T.66 Ligand excluded by PLIP SO4.5: 4 residues within 4Å: Chain A: R.106, K.127, G.128, D.129 Ligand excluded by PLIP SO4.6: 4 residues within 4Å: Chain A: S.143, H.144, D.145, K.337 Ligand excluded by PLIP SO4.7: 4 residues within 4Å: Chain A: E.257, N.260, R.264, S.298 Ligand excluded by PLIP SO4.9: 5 residues within 4Å: Chain B: T.184, D.186, R.199, R.235 Ligands: NAD.8 Ligand excluded by PLIP SO4.10: 5 residues within 4Å: Chain B: S.153, T.155, T.212, G.213, A.214 Ligand excluded by PLIP SO4.11: 5 residues within 4Å: Chain B: P.131, T.132, Y.133, N.138, L.220 Ligand excluded by PLIP SO4.12: 3 residues within 4Å: Chain B: F.255, A.256, V.303 Ligand excluded by PLIP SO4.13: 5 residues within 4Å: Chain B: V.285, R.288 Chain C: S.51, T.52, G.54 Ligand excluded by PLIP SO4.15: 5 residues within 4Å: Chain C: T.184, D.186, R.199, R.235 Ligands: NAD.14 Ligand excluded by PLIP SO4.16: 5 residues within 4Å: Chain C: S.153, T.155, T.212, G.213, A.214 Ligand excluded by PLIP SO4.17: 3 residues within 4Å: Chain C: G.64, E.65, T.66 Ligand excluded by PLIP SO4.18: 4 residues within 4Å: Chain C: R.106, K.127, G.128, D.129 Ligand excluded by PLIP SO4.19: 4 residues within 4Å: Chain C: S.143, H.144, D.145, K.337 Ligand excluded by PLIP SO4.20: 4 residues within 4Å: Chain C: E.257, N.260, R.264, S.298 Ligand excluded by PLIP SO4.22: 5 residues within 4Å: Chain D: T.184, D.186, R.199, R.235 Ligands: NAD.21 Ligand excluded by PLIP SO4.23: 5 residues within 4Å: Chain D: S.153, T.155, T.212, G.213, A.214 Ligand excluded by PLIP SO4.24: 5 residues within 4Å: Chain D: P.131, T.132, Y.133, N.138, L.220 Ligand excluded by PLIP SO4.25: 3 residues within 4Å: Chain D: F.255, A.256, V.303 Ligand excluded by PLIP SO4.26: 5 residues within 4Å: Chain A: S.51, T.52, G.54 Chain D: V.285, R.288 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fermani, S. et al., Structure of photosynthetic glyceraldehyde-3-phosphate dehydrogenase (isoform A4) from Arabidopsis thaliana in complex with NAD. Acta Crystallogr.,Sect.F (2010)

Release Date

2010-06-09

Peptides

Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
O

B
Q

C
O

D
Q

Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic

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