SMTL ID : 6e8z.1

Binary complex of Human glycerol 3-phosphate dehydrogenase with NAD

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

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

NAD.1: 22 residues within 4Å: Chain A: G.10, S.11, G.12, N.13, W.14, G.15, W.39, F.41, Y.63, V.92, V.93, P.94, H.95, F.97, I.101, L.118, I.119, K.120, N.151, I.152, A.153 Ligands: EDO.5 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:W.14 Hydrogen bonds: A:S.11, A:S.11, A:S.11, A:N.13, A:N.13, A:W.14, A:G.15, A:V.93, A:K.120, A:K.120, A:A.153 Water bridges: A:G.12, A:N.13, A:F.41, A:Y.63 pi-Stacking: A:W.14, A:F.41, A:F.41, A:F.97, A:F.97 NAD.7: 22 residues within 4Å: Chain B: G.10, S.11, G.12, N.13, W.14, G.15, W.39, F.41, E.43, Y.63, V.92, V.93, P.94, H.95, F.97, I.101, L.118, I.119, K.120, N.151, I.152, A.153 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:S.11, B:S.11, B:N.13, B:N.13, B:W.14, B:K.120, B:A.153 Water bridges: B:G.12, B:G.15, B:F.41, B:Y.63, B:S.154, B:S.154 pi-Stacking: B:W.14, B:W.14, B:F.41, B:F.41, B:F.97, B:F.97

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 7 residues within 4Å: Chain A: K.130, L.131, E.134, D.195, F.242, C.243, S.244 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:L.131, A:E.134, A:E.134, A:D.195, A:S.244, A:S.244, A:S.244 PO4.8: 7 residues within 4Å: Chain B: K.130, L.131, E.134, D.195, F.242, C.243, S.244 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:L.131, B:E.134, B:E.134, B:S.244, B:S.244

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

EDO.3: 8 residues within 4Å: Chain A: M.233, E.234, A.237, K.318, F.319, H.345, P.346, E.347 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.347 EDO.4: 5 residues within 4Å: Chain A: K.240, C.243, G.245, P.246, V.247 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.247, A:V.247 EDO.5: 11 residues within 4Å: Chain A: K.120, G.149, A.150, N.151, I.152, K.204, D.260, T.263, T.264 Chain B: N.222 Ligands: NAD.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.120, A:N.151, A:K.204, A:D.260 EDO.9: 8 residues within 4Å: Chain B: M.233, E.234, A.237, K.318, F.319, H.345, P.346, E.347 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.347, B:E.347

2 x K: POTASSIUM ION(Non-covalent)

K.6: 6 residues within 4Å: Chain A: A.26, A.27, L.29, A.30, F.32, P.34 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:A.26, A:L.29, A:F.32 K.10: 6 residues within 4Å: Chain B: A.26, A.27, L.29, A.30, F.32, P.34 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:A.26, B:L.29, B:F.32, H2O.8

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mydy, L.S. et al., Human Glycerol 3-Phosphate Dehydrogenase: X-ray Crystal Structures That Guide the Interpretation of Mutagenesis Studies. Biochemistry (2019)

Release Date

2019-01-30

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

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