SMTL ID : 6gfr.1

cyanobacterial GAPDH with NAD

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.92 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 20 residues within 4Å: Chain A: G.10, F.11, G.12, R.13, I.14, N.37, D.38, T.39, D.82, R.83, A.101, T.102, G.103, F.105, T.125, A.126, C.156, T.186, N.319, Y.323 24 PLIP interactions: 22 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:I.14, A:Y.323 Hydrogen bonds: A:F.11, A:F.11, A:R.13, A:I.14, A:N.37, A:T.39, A:R.83, A:N.319 Water bridges: A:N.9, A:N.9, A:G.12, A:G.15, A:R.16, A:R.16, A:G.103, A:T.125, A:G.187, A:G.187, A:G.187, A:R.201, D:S.195, D:S.195 NAD.4: 20 residues within 4Å: Chain B: G.10, F.11, G.12, R.13, I.14, N.37, D.38, T.39, D.82, R.83, A.101, T.102, G.103, F.105, T.125, A.126, C.156, N.319, Y.323 Ligands: ACT.6 23 PLIP interactions: 20 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:I.14, B:Y.323 Hydrogen bonds: B:F.11, B:F.11, B:R.13, B:I.14, B:N.37, B:D.38, B:T.39, B:R.83, B:N.319 Water bridges: B:N.9, B:G.12, B:G.15, B:R.16, B:R.16, B:G.103, B:T.125, B:G.187, B:G.187, C:S.195, C:S.195, C:S.195 NAD.7: 20 residues within 4Å: Chain C: G.10, F.11, G.12, R.13, I.14, N.37, D.38, T.39, D.82, R.83, A.101, T.102, G.103, F.105, T.125, A.126, C.156, T.186, N.319, Y.323 27 PLIP interactions: 25 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:I.14, C:Y.323 Hydrogen bonds: C:F.11, C:F.11, C:R.13, C:I.14, C:N.37, C:D.38, C:T.39, C:R.83, C:T.125, C:N.319 Water bridges: C:N.9, C:N.9, C:G.12, C:G.15, C:R.16, C:R.16, C:T.39, C:G.103, C:T.125, C:G.187, C:G.187, C:G.187, C:R.201, B:S.195, B:S.195 NAD.10: 20 residues within 4Å: Chain D: G.10, F.11, G.12, R.13, I.14, N.37, D.38, T.39, D.82, R.83, A.101, T.102, G.103, F.105, T.125, A.126, C.156, N.319, Y.323 Ligands: ACT.12 23 PLIP interactions: 20 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: D:I.14, D:Y.323 Hydrogen bonds: D:F.11, D:F.11, D:R.13, D:I.14, D:N.37, D:T.39, D:R.83, D:T.125, D:N.319 Water bridges: D:N.9, D:G.12, D:G.15, D:R.16, D:R.16, D:G.103, D:T.125, D:G.187, D:G.187, A:S.195, A:S.195, A:S.195

6 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 7 residues within 4Å: Chain A: S.155, C.156, T.157, H.183, T.214, G.215, R.237 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.155, A:T.157, A:T.157, A:G.215 Water bridges: A:C.156, A:R.237 Salt bridges: A:H.183 ACT.5: 9 residues within 4Å: Chain B: S.155, C.156, T.157, H.183, R.201, S.213, T.214, G.215, R.237 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.155, B:T.157, B:T.157, B:T.214, B:G.215 Water bridges: B:S.213 Salt bridges: B:H.183 ACT.6: 3 residues within 4Å: Chain B: T.186, D.188 Ligands: NAD.4 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:D.188 Hydrogen bonds: B:T.186, B:D.188 ACT.8: 7 residues within 4Å: Chain C: S.155, C.156, T.157, H.183, T.214, G.215, R.237 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:S.155, C:T.157, C:T.157, C:T.214, C:G.215 Water bridges: C:C.156 Salt bridges: C:H.183 ACT.11: 9 residues within 4Å: Chain D: S.155, C.156, T.157, H.183, R.201, S.213, T.214, G.215, R.237 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:S.155, D:T.157, D:T.157, D:G.215 Water bridges: D:S.213 Salt bridges: D:H.183 ACT.12: 3 residues within 4Å: Chain D: T.186, D.188 Ligands: NAD.10 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:D.188 Hydrogen bonds: D:D.188

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: G.307, N.309 Chain C: Q.251 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:G.307, H2O.19, H2O.22, H2O.22 MG.9: 3 residues within 4Å: Chain A: Q.251 Chain C: G.307, N.309 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:G.307, H2O.4, H2O.6, H2O.7

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

McFarlane, C.R. et al., Structural basis of light-induced redox regulation in the Calvin-Benson cycle in cyanobacteria. Proc.Natl.Acad.Sci.USA (2019)

Release Date

2019-05-08

Peptides

Glyceraldehyde-3-phosphate dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Glyceraldehyde-3-phosphate dehydrogenase

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