SMTL ID : 4rfl.1 (1 other biounit)

Crystal structure of G1PDH with NADPH from Methanocaldococcus jannaschii

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.1: 23 residues within 4Å: Chain A: G.72, K.73, N.74, T.75, Y.78, Y.88, G.113, G.114, R.115, D.118, T.136, T.137, S.139, N.140, G.142, S.149, S.173, P.174, L.177, H.266, H.283 Ligands: ZN.3, EDO.7 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:N.140 Hydrogen bonds: A:N.74, A:N.74, A:T.75, A:T.75, A:Y.78, A:Y.78, A:Y.88, A:G.114, A:R.115, A:R.115, A:R.115, A:D.118, A:S.139, A:S.149 Water bridges: A:G.72, A:K.73, A:K.73, A:G.113, A:G.113, A:S.116, A:D.118, A:H.266 NDP.10: 23 residues within 4Å: Chain B: G.72, K.73, N.74, T.75, Y.78, Y.88, G.113, G.114, R.115, D.118, T.136, T.137, S.139, N.140, G.142, S.149, S.173, P.174, L.177, H.262, H.266, H.283 Ligands: ZN.12 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:N.140 Hydrogen bonds: B:N.74, B:N.74, B:T.75, B:Y.88, B:G.114, B:R.115, B:R.115, B:T.136, B:S.139, B:N.140, B:S.149 Water bridges: B:G.72, B:G.72, B:K.73, B:K.77, B:G.113, B:S.116, B:D.118

2 x K: POTASSIUM ION(Non-covalent)

K.2: 5 residues within 4Å: Chain A: D.141, D.184, S.187, N.188, A.257 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.141, A:D.184, A:A.257 K.11: 6 residues within 4Å: Chain B: D.141, D.184, S.187, N.188, A.257, H.262 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.141, B:D.184, B:A.257

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain A: D.141, D.184, H.262, H.283 Ligands: NDP.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.184, A:H.262, A:H.283, H2O.1 ZN.12: 5 residues within 4Å: Chain B: D.141, D.184, H.262, H.283 Ligands: NDP.10 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.184, B:H.262, B:H.283, H2O.6

8 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 10 residues within 4Å: Chain A: I.38, I.39, V.40, P.146, M.156, V.157, D.158, A.159, A.249, N.252 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.40, A:V.157, A:A.159, A:A.249 EDO.5: 4 residues within 4Å: Chain A: I.38, I.39 Chain B: T.45, I.47 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:I.47, A:I.38 EDO.6: 5 residues within 4Å: Chain A: T.45, I.46, I.47 Chain B: I.38, I.39 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:I.38, A:I.47 EDO.7: 7 residues within 4Å: Chain A: S.154, S.254, S.258, H.262, H.266, R.346 Ligands: NDP.1 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.154, A:S.254, A:S.254, A:S.258, A:H.266, A:R.346 Water bridges: A:R.346, A:R.348 EDO.8: 5 residues within 4Å: Chain A: K.300, E.360, K.363, L.364, E.367 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.300, A:E.367 EDO.9: 4 residues within 4Å: Chain A: R.175, S.179, Y.233, V.319 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.175, A:S.179 Water bridges: A:L.230, A:Y.233 EDO.13: 2 residues within 4Å: Chain B: K.215, K.219 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.215 EDO.14: 4 residues within 4Å: Chain B: C.79, R.80, F.81, F.82 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.80, B:F.81

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Carbone, V. et al., Structure and Evolution of the Archaeal Lipid Synthesis Enzyme sn-Glycerol-1-phosphate Dehydrogenase. J.Biol.Chem. (2015)

Release Date

2015-07-22

Peptides

Glycerol-1-phosphate dehydrogenase [NAD(P)+]: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glycerol-1-phosphate dehydrogenase [NAD(P)+]

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