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

Crystal structure of the Methanocaldococcus jannaschii G1PDH with NADPH and DHAP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.23 Å

Oligo State

homo-dimer

Ligands

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

NDP.1: 26 residues within 4Å: Chain A: G.69, K.70, N.71, T.72, Y.75, Y.85, G.110, G.111, R.112, D.115, K.118, T.133, T.134, S.136, N.137, G.139, S.142, I.144, V.145, S.146, S.170, P.171, L.174, H.280 Ligands: 13P.4, EDO.10 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:N.71, A:N.71, A:T.72, A:Y.75, A:Y.85, A:G.111, A:R.112, A:R.112, A:T.133, A:S.136, A:N.137, A:S.142, A:I.144, A:S.146 Water bridges: A:K.70, A:K.70, A:T.72, A:T.72, A:G.110, A:S.113, A:D.115, A:H.280 pi-Stacking: A:H.280 NDP.13: 25 residues within 4Å: Chain B: G.69, K.70, N.71, T.72, Y.75, Y.85, G.110, G.111, R.112, D.115, K.118, T.133, T.134, S.136, N.137, G.139, S.142, I.144, S.146, S.170, P.171, L.174, H.280 Ligands: ZN.15, 1GP.16 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:N.137 Hydrogen bonds: B:N.71, B:N.71, B:T.72, B:T.72, B:Y.85, B:Y.85, B:G.111, B:R.112, B:R.112, B:T.133, B:S.136, B:N.137, B:S.142, B:I.144, B:S.146 Water bridges: B:G.69, B:G.69, B:K.70, B:G.110, B:S.113, B:D.115 pi-Stacking: B:H.280

2 x K: POTASSIUM ION(Non-covalent)

K.2: 7 residues within 4Å: Chain A: D.138, D.181, S.184, N.185, A.254, H.259 Ligands: 13P.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.138, A:D.181, A:A.254 K.14: 7 residues within 4Å: Chain B: D.138, D.181, S.184, N.185, A.254, H.259 Ligands: 1GP.16 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.138, B:D.181, B:A.254

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain A: D.138, D.181, H.259, H.280 Ligands: 13P.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.181, A:H.259, A:H.280 ZN.15: 6 residues within 4Å: Chain B: D.138, D.181, H.259, H.280 Ligands: NDP.13, 1GP.16 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.181, B:H.259, B:H.280

1 x 13P: 1,3-DIHYDROXYACETONEPHOSPHATE(Non-covalent)

13P.4: 14 residues within 4Å: Chain A: D.138, Q.149, S.151, D.181, S.251, A.254, S.255, H.259, H.263, H.280, R.343 Ligands: NDP.1, K.2, ZN.3 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:D.138, A:Q.149, A:S.151, A:S.151, A:S.251, A:S.255, A:R.343 Water bridges: A:S.146, A:S.146, A:S.255 Salt bridges: A:H.263

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

EDO.5: 7 residues within 4Å: Chain A: I.36, V.37, P.143, V.154, A.156, A.246, N.249 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.37, A:V.154, A:A.156, A:N.249 EDO.6: 8 residues within 4Å: Chain A: K.118, A.121, Y.122, F.128, V.154, D.155, A.156, P.157 2 PLIP interactions: 2 interactions with chain A Water bridges: A:A.121, A:F.128 EDO.7: 7 residues within 4Å: Chain A: I.49, N.50, K.51, I.52, E.53, F.78, Y.80 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.50, A:E.53 Water bridges: A:E.54 EDO.8: 5 residues within 4Å: Chain A: R.172, L.175, S.176, Y.230, V.316 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.172, A:S.176 EDO.9: 4 residues within 4Å: Chain A: Y.122, K.123, L.124, G.125 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.122 EDO.10: 3 residues within 4Å: Chain A: P.171, L.174 Ligands: NDP.1 No protein-ligand interaction detected (PLIP) EDO.11: 7 residues within 4Å: Chain A: Y.293, L.294, K.297, E.357, K.360, L.361, E.364 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.364 EDO.12: 4 residues within 4Å: Chain A: I.35, I.36 Chain B: T.42, I.44 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:I.35, B:I.44 EDO.17: 4 residues within 4Å: Chain B: C.76, R.77, F.78, F.79 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.77, B:F.78, B:F.78 EDO.18: 8 residues within 4Å: Chain B: I.36, V.37, P.143, M.153, V.154, A.156, A.246, N.249 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:V.37, B:V.154, B:A.156, B:N.249 EDO.19: 5 residues within 4Å: Chain B: Y.293, K.297, E.357, L.361, E.364 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.297, B:E.357, B:E.364 EDO.20: 4 residues within 4Å: Chain A: L.59 Chain B: L.59, P.127, I.158 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:L.59, B:L.59

1 x 1GP: SN-GLYCEROL-1-PHOSPHATE(Non-covalent)

1GP.16: 14 residues within 4Å: Chain B: D.138, S.146, Q.149, S.151, S.251, A.254, S.255, H.259, H.263, H.280, R.343 Ligands: NDP.13, K.14, ZN.15 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:D.138, B:S.146, B:S.151, B:S.251, B:S.255, B:H.280 Water bridges: B:R.345 Salt bridges: B:H.263, B:R.343

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glycerol-1-phosphate dehydrogenase

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