SMTL ID : 6gfp.1

cyanobacterial GAPDH with NADP bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.54 Å

Oligo State

homo-tetramer

Ligands

4 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.1: 24 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, V.104, F.105, T.125, A.126, C.156, T.186, N.319, Y.323 Chain D: S.195 Ligands: NAD.2, FMT.4 29 PLIP interactions: 25 interactions with chain A, 4 interactions with chain D Hydrophobic interactions: A:I.14, A:I.14, A:Y.323 Hydrogen bonds: A:F.11, A:R.13, A:I.14, A:N.37, A:T.39, A:R.83, A:R.83, A:N.319, D:S.195 Water bridges: A:N.9, A:N.9, A:G.12, A:G.15, A:R.16, A:T.39, A:R.83, A:R.83, A:R.83, A:R.83, A:G.103, A:G.187, A:G.187, A:G.187, D:S.195, D:S.195, D:S.195 NAP.5: 21 residues within 4Å: Chain B: G.10, F.11, G.12, R.13, I.14, N.37, D.38, T.39, R.83, A.101, T.102, G.103, V.104, F.105, T.125, A.126, C.156, N.319, Y.323 Chain C: S.195 Ligands: NAD.6 28 PLIP interactions: 26 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:I.14, B:I.14, B:Y.323 Hydrogen bonds: B:F.11, B:R.13, B:I.14, B:N.37, B:D.38, B:T.39, B:T.39, B:N.319 Water bridges: B:N.9, B:N.9, B:G.12, B:G.15, B:R.16, B:S.40, B:R.83, B:R.83, B:R.83, B:R.83, B:G.103, B:G.187, B:G.187, B:G.187, B:G.187, C:S.195, C:S.195 NAP.9: 24 residues within 4Å: Chain B: S.195 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, V.104, F.105, T.125, A.126, C.156, T.186, N.319, Y.323 Ligands: NAD.10, FMT.12 31 PLIP interactions: 27 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:I.14, C:I.14, C:Y.323 Hydrogen bonds: C:F.11, C:R.13, C:I.14, C:N.37, C:D.38, C:T.39, C:T.39, C:R.83, C:R.83, C:T.125, C:N.319, B:S.195 Water bridges: C:N.9, C:N.9, C:G.12, C:G.15, C:R.16, C:R.83, C:R.83, C:R.83, C:R.83, C:G.103, C:G.187, C:G.187, C:G.187, B:S.195, B:S.195, B:S.195 NAP.13: 21 residues within 4Å: Chain A: S.195 Chain D: G.10, F.11, G.12, R.13, I.14, N.37, D.38, T.39, R.83, A.101, T.102, G.103, V.104, F.105, T.125, A.126, C.156, N.319, Y.323 Ligands: NAD.14 29 PLIP interactions: 27 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:I.14, D:I.14, D:Y.323 Hydrogen bonds: D:F.11, D:R.13, D:I.14, D:N.37, D:T.39, D:T.39, D:T.39, D:T.125, D:N.319 Water bridges: D:N.9, D:N.9, D:G.12, D:G.15, D:R.16, D:S.40, D:R.83, D:R.83, D:R.83, D:R.83, D:G.103, D:G.187, D:G.187, D:G.187, D:G.187, A:S.195, A:S.195

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

NAD.2: 22 residues within 4Å: Chain A: G.10, F.11, G.12, R.13, I.14, N.37, D.38, T.39, R.83, A.101, T.102, G.103, F.105, T.125, A.126, C.156, T.186, N.319, E.320, Y.323 Ligands: NAP.1, FMT.4 21 PLIP interactions: 20 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:I.14, A:Y.323 Hydrogen bonds: A:F.11, A:R.13, A:I.14, A:D.38, A:T.39, A:R.83, A:N.319, D:S.195 Water bridges: A:N.9, A:G.12, A:R.16, A:R.16, A:R.83, A:G.103, A:G.187, A:G.187, A:G.187, A:G.187, A:G.187 NAD.6: 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, T.125, A.126, C.156, T.186, N.319, Y.323 Ligands: NAP.5 24 PLIP interactions: 23 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:I.14, B:Y.323 Hydrogen bonds: B:R.13, B:I.14, B:N.37, B:D.38, B:D.38, B:T.39, B:N.319 Water bridges: B:N.9, B:N.9, B:G.12, B:G.15, B:R.16, B:R.83, B:R.83, B:R.83, B:G.103, B:G.187, B:G.187, B:G.187, B:G.187, B:G.187, C:S.195 NAD.10: 22 residues within 4Å: Chain C: G.10, F.11, G.12, R.13, I.14, N.37, D.38, T.39, R.83, A.101, T.102, G.103, F.105, T.125, A.126, C.156, T.186, N.319, E.320, Y.323 Ligands: NAP.9, FMT.12 23 PLIP interactions: 22 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:I.14, C:Y.323 Hydrogen bonds: C:F.11, C:R.13, C:I.14, C:D.38, C:D.38, C:T.39, C:R.83, C:T.125, C:N.319, B:S.195 Water bridges: C:N.9, C:G.12, C:R.16, C:R.16, C:R.83, C:G.103, C:G.187, C:G.187, C:G.187, C:G.187, C:G.187 NAD.14: 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, T.125, A.126, C.156, T.186, N.319, Y.323 Ligands: NAP.13 23 PLIP interactions: 22 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:I.14, D:Y.323 Hydrogen bonds: D:R.13, D:I.14, D:N.37, D:D.38, D:T.39, D:T.125, D:N.319 Water bridges: D:N.9, D:G.12, D:G.15, D:R.16, D:R.83, D:R.83, D:R.83, D:G.103, D:G.187, D:G.187, D:G.187, D:G.187, D:G.187, A:S.195

4 x MLI: MALONATE ION(Non-functional Binders)

MLI.3: 11 residues within 4Å: Chain A: S.155, C.156, T.157, H.183, R.201, S.213, T.214, G.215, A.216, R.237 Ligands: FMT.4 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:S.155, A:T.157, A:T.157, A:G.215, A:A.216 Water bridges: A:R.201, A:R.201, A:R.201, A:R.201, A:R.237 Salt bridges: A:H.183, A:R.201, A:R.237 MLI.7: 10 residues within 4Å: Chain B: S.155, C.156, T.157, H.183, R.201, S.213, T.214, G.215, A.216, R.237 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:S.155, B:T.157, B:T.157, B:T.214, B:G.215, B:A.216 Water bridges: B:T.186, B:T.186, B:R.201, B:R.201, B:R.201, B:R.201, B:R.237 Salt bridges: B:H.183, B:R.201, B:R.237 MLI.11: 11 residues within 4Å: Chain C: S.155, C.156, T.157, H.183, R.201, S.213, T.214, G.215, A.216, R.237 Ligands: FMT.12 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:S.155, C:T.157, C:T.157, C:T.214, C:G.215, C:A.216 Water bridges: C:R.201, C:R.201, C:R.201, C:R.201, C:R.237 Salt bridges: C:H.183, C:R.201, C:R.237 MLI.15: 10 residues within 4Å: Chain D: S.155, C.156, T.157, H.183, R.201, S.213, T.214, G.215, A.216, R.237 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:S.155, D:T.157, D:T.157, D:G.215, D:A.216 Water bridges: D:T.186, D:R.201, D:R.201, D:R.201, D:R.201, D:R.237 Salt bridges: D:H.183, D:R.201, D:R.237

2 x FMT: FORMIC ACID(Non-functional Binders)

FMT.4: 7 residues within 4Å: Chain A: T.186, D.188, R.201, R.237 Ligands: NAP.1, NAD.2, MLI.3 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:T.186, A:R.201, A:R.237, A:R.237 Water bridges: A:G.187, A:D.188, A:D.188, A:R.201 FMT.12: 7 residues within 4Å: Chain C: T.186, D.188, R.201, R.237 Ligands: NAP.9, NAD.10, MLI.11 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:R.201, C:R.237, C:R.237 Water bridges: C:G.187, C:D.188, C:D.188, C:R.201

2 x MG: MAGNESIUM ION(Non-covalent)

MG.8: 1 residues within 4Å: Chain B: S.116 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:S.116, H2O.18, H2O.22, H2O.22 MG.16: 1 residues within 4Å: Chain D: S.116 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:S.116, H2O.42, H2O.46, H2O.46

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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