SMTL ID : 1x0x.2 (1 other biounit)

Co-Structure of Homo Sapiens Glycerol-3-Phosphate Dehydrogenase 1 complex with NAD

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

homo-dimer

Ligands

10 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 4 residues within 4Å: Chain A: K.25, G.71, H.72, K.73 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.73, A:A.162 Water bridges: A:G.71 Salt bridges: A:K.25, A:H.72 SO4.2: 6 residues within 4Å: Chain A: K.209, N.210, T.269, G.273, R.274, N.275 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:R.274, A:N.275 Water bridges: A:K.209, A:K.209, A:K.209, A:K.209, A:R.274 Salt bridges: A:K.209, A:R.274 SO4.3: 4 residues within 4Å: Chain A: K.245, V.252, S.253, S.254 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.254, A:S.254 Water bridges: A:K.245, A:K.245, A:K.245, A:K.245, A:A.255 Salt bridges: A:K.245 SO4.4: 2 residues within 4Å: Chain A: R.276, K.277 7 PLIP interactions: 7 interactions with chain A Water bridges: A:G.272, A:R.276, A:R.276, A:R.276, A:K.277 Salt bridges: A:R.276, A:K.277 SO4.5: 5 residues within 4Å: Chain A: N.18, Y.68, L.69, S.159, Q.300 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.18, A:N.18 Water bridges: A:P.70, A:S.159, A:S.159, A:S.159, A:S.159, A:Q.300 SO4.7: 4 residues within 4Å: Chain B: K.25, G.71, H.72, K.73 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.73, B:A.162 Water bridges: B:G.71 Salt bridges: B:K.25, B:H.72 SO4.8: 6 residues within 4Å: Chain B: K.209, N.210, T.269, G.273, R.274, N.275 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:R.274, B:N.275 Water bridges: B:K.209, B:K.209, B:K.209, B:K.209, B:R.274 Salt bridges: B:K.209, B:R.274 SO4.9: 4 residues within 4Å: Chain B: K.245, V.252, S.253, S.254 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:S.254, B:S.254 Water bridges: B:K.245, B:K.245, B:K.245, B:K.245, B:A.255 Salt bridges: B:K.245 SO4.10: 2 residues within 4Å: Chain B: R.276, K.277 7 PLIP interactions: 7 interactions with chain B Water bridges: B:G.272, B:R.276, B:R.276, B:R.276, B:K.277 Salt bridges: B:R.276, B:K.277 SO4.11: 5 residues within 4Å: Chain B: N.18, Y.68, L.69, S.159, Q.300 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:N.18, B:N.18 Water bridges: B:P.70, B:S.159, B:S.159, B:S.159, B:S.159, B:Q.300

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

NAD.6: 23 residues within 4Å: Chain A: S.16, G.17, N.18, W.19, G.20, W.44, F.46, Y.68, V.97, V.98, P.99, F.102, L.123, I.124, K.125, N.156, I.157, A.158, R.274, G.299, Q.300, K.301, Q.303 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:W.19 Hydrogen bonds: A:S.16, A:G.17, A:G.17, A:N.18, A:N.18, A:W.19, A:G.20, A:V.98, A:K.125, A:A.158, A:K.301 Water bridges: A:F.46, A:K.125, A:N.210, A:R.274, A:R.274, A:K.301, A:Q.303 Salt bridges: A:R.274, A:R.274 pi-Stacking: A:W.19, A:F.46, A:F.102, A:F.102 pi-Cation interactions: A:K.209 NAD.12: 23 residues within 4Å: Chain B: S.16, G.17, N.18, W.19, G.20, W.44, F.46, Y.68, V.97, V.98, P.99, F.102, L.123, I.124, K.125, N.156, I.157, A.158, R.274, G.299, Q.300, K.301, Q.303 26 PLIP interactions: 26 interactions with chain B Hydrophobic interactions: B:W.19 Hydrogen bonds: B:S.16, B:G.17, B:G.17, B:N.18, B:N.18, B:W.19, B:G.20, B:V.98, B:K.125, B:A.158, B:K.301 Water bridges: B:F.46, B:K.125, B:N.210, B:R.274, B:R.274, B:K.301, B:Q.303 Salt bridges: B:R.274, B:R.274 pi-Stacking: B:W.19, B:F.46, B:F.102, B:F.102 pi-Cation interactions: B:K.209

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ou, X. et al., Crystal Structures of Human Glycerol 3-phosphate Dehydrogenase 1 (GPD1). J.Mol.Biol. (2006)

Release Date

2006-04-11

Peptides

Glycerol-3-phosphate dehydrogenase [NAD+], cytoplasmic: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Glycerol-3-phosphate dehydrogenase [NAD+], cytoplasmic

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