SMTL ID : 6gfq.1

cyanobacterial GAPDH with NAD and CP12 bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

hetero-4-2-mer

Ligands

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

NAD.1: 18 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, N.319, Y.323 28 PLIP interactions: 27 interactions with chain A, 1 interactions with chain F 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:D.38, A:T.39, A:T.39, A:R.83, A:N.319 Water bridges: A:N.9, A:N.9, A:G.12, A:G.15, A:N.45, A:R.83, A:R.83, A:R.83, A:R.83, A:R.83, A:G.103, A:T.125, A:G.187, A:G.187, A:G.187, F:E.71 NAD.3: 23 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, E.320, Y.323 Chain C: D.68, Y.75, D.76 27 PLIP interactions: 21 interactions with chain B, 1 interactions with chain D, 5 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, C:Y.75, C:D.76 Water bridges: B:N.9, B:N.9, B:G.12, B:G.15, B:R.16, B:S.40, B:N.45, B:G.103, B:T.125, B:G.187, D:S.195, C:R.73, C:I.74, C:D.77 NAD.5: 18 residues within 4Å: 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, F.105, T.125, A.126, C.156, N.319, Y.323 29 PLIP interactions: 27 interactions with chain D, 2 interactions with chain C 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:T.39, D:R.83, D:T.125, D:N.319 Water bridges: D:N.9, D:N.9, D:G.12, D:G.15, D:N.45, D:R.83, D:R.83, D:R.83, D:R.83, D:R.83, D:G.103, D:T.125, D:G.187, D:G.187, D:G.187, C:E.71, C:E.71 NAD.7: 23 residues within 4Å: Chain E: 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, E.320, Y.323 Chain F: D.68, Y.75, D.76 27 PLIP interactions: 22 interactions with chain E, 4 interactions with chain F, 1 interactions with chain A Hydrophobic interactions: E:I.14, E:Y.323 Hydrogen bonds: E:F.11, E:F.11, E:R.13, E:I.14, E:N.37, E:T.39, E:R.83, E:T.125, E:N.319, F:D.76 Water bridges: E:N.9, E:N.9, E:G.12, E:G.15, E:R.16, E:T.39, E:S.40, E:N.45, E:G.103, E:T.125, E:G.187, F:R.73, F:I.74, F:D.77, A:S.195

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: G.307, N.309 Chain D: Q.251 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:G.307, H2O.8, H2O.23, H2O.23, H2O.26 MG.4: 3 residues within 4Å: Chain B: G.307, N.309 Chain E: Q.251 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:G.307, H2O.16, H2O.17, H2O.17, H2O.34 MG.6: 3 residues within 4Å: Chain A: Q.251 Chain D: G.307, N.309 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:G.307, H2O.4, H2O.5, H2O.8, H2O.26 MG.8: 3 residues within 4Å: Chain B: Q.251 Chain E: G.307, N.309 5 PLIP interactions: 1 interactions with chain E, 4 Ligand-Water interactions Metal complexes: E:G.307, H2O.15, H2O.35, H2O.35, H2O.36

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: ABDE
CP12 polypeptide: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D
A

E
B

C
C

F
C

Glyceraldehyde-3-phosphate dehydrogenase

CP12 polypeptide

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