SMTL ID : 1wpq.1

Ternary Complex Of Glycerol 3-phosphate Dehydrogenase 1 with NAD and dihydroxyactone

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: K.20, G.66, H.67, K.68 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.68 Water bridges: A:H.67, A:H.67, A:E.159, A:E.159 Salt bridges: A:K.20, A:H.67 SO4.2: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.158 SO4.3: 2 residues within 4Å: Chain A: R.271, K.272 7 PLIP interactions: 7 interactions with chain A Water bridges: A:G.267, A:G.268, A:R.271, A:K.272, A:K.272 Salt bridges: A:R.271, A:K.272 SO4.4: 3 residues within 4Å: Chain A: K.178, Q.182, R.187 9 PLIP interactions: 1 interactions with chain B, 8 interactions with chain A Water bridges: B:E.347, A:K.178, A:K.178, A:K.178, A:Q.182, A:R.187 Hydrogen bonds: A:Q.182 Salt bridges: A:K.178, A:R.187 SO4.5: 2 residues within 4Å: Chain A: V.247, S.248 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.249 Water bridges: A:V.247, A:S.249 SO4.6: 3 residues within 4Å: Chain A: P.346, E.347, H.348 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.347, A:H.348 SO4.9: 4 residues within 4Å: Chain B: K.240, V.247, S.248, S.249 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.249 Water bridges: B:A.250 Salt bridges: B:K.240

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

13P.7: 10 residues within 4Å: Chain A: K.120, G.149, K.204, N.205, D.260, T.264, G.268, R.269, N.270 Ligands: NAD.8 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:K.120, A:K.204, A:R.269, A:N.270, A:N.270 Water bridges: A:G.149, A:N.151 Salt bridges: A:K.204, A:R.269 13P.10: 8 residues within 4Å: Chain B: K.120, K.204, N.205, T.264, G.268, R.269, N.270 Ligands: NAD.11 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:K.204, B:R.269, B:N.270, B:N.270 Water bridges: B:K.120, B:T.264, B:G.268, B:R.269, B:R.269 Salt bridges: B:K.204, B:R.269

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

NAD.8: 25 residues within 4Å: Chain A: S.11, G.12, N.13, W.14, G.15, W.39, F.41, E.43, Y.63, V.92, V.93, P.94, F.97, L.118, I.119, K.120, N.151, I.152, A.153, R.269, G.294, Q.295, K.296, Q.298 Ligands: 13P.7 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:W.14 Hydrogen bonds: A:S.11, A:G.12, A:N.13, A:N.13, A:W.14, A:G.15, A:E.43, A:V.93, A:K.120, A:A.153, A:K.296 Water bridges: A:S.11, A:S.11, A:S.154 Salt bridges: A:R.269, A:R.269 pi-Stacking: A:W.14, A:F.41, A:F.41, A:F.97, A:F.97 NAD.11: 24 residues within 4Å: Chain B: S.11, G.12, N.13, W.14, G.15, W.39, F.41, Y.63, V.92, V.93, P.94, F.97, L.118, I.119, K.120, N.151, I.152, A.153, R.269, G.294, Q.295, K.296, Q.298 Ligands: 13P.10 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:W.14 Hydrogen bonds: B:S.11, B:S.11, B:G.12, B:G.12, B:N.13, B:N.13, B:W.14, B:G.15, B:V.93, B:K.120, B:A.153, B:K.296, B:Q.298 Water bridges: B:S.11, B:N.13, B:F.41 Salt bridges: B:R.269, B:R.269 pi-Stacking: B:W.14, B:F.41, B:F.41, B:F.97

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
B

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