SMTL ID : 6e90.1 (1 other biounit)

Ternary complex of human glycerol 3-phosphate dehydrogenase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-dimer

Ligands

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

NAD.1: 28 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, H.95, F.97, I.101, L.118, I.119, K.120, N.151, I.152, A.153, N.205, R.269, G.294, Q.295, K.296, Q.298 Ligands: 13P.2 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:W.14 Hydrogen bonds: A:S.11, A:S.11, A:G.12, A:N.13, A:N.13, A:W.14, A:G.15, A:K.120, A:A.153, A:K.296, A:Q.298 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.5: 21 residues within 4Å: Chain B: 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 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:W.14 Hydrogen bonds: B:S.11, B:G.12, B:N.13, B:N.13, B:W.14, B:G.15, B:V.93, B:K.120, B:K.120, B:A.153 Water bridges: B:S.154 pi-Stacking: B:W.14, B:F.41, B:F.41, B:F.97, B:F.97

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

13P.2: 14 residues within 4Å: Chain A: K.120, G.149, A.150, N.151, I.152, K.204, N.205, D.260, T.263, T.264, G.268, R.269, N.270 Ligands: NAD.1 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:K.120, A:G.149, A:N.151, A:K.204, A:R.269, A:N.270, A:N.270 Water bridges: A:N.270 Salt bridges: A:K.204, A:R.269

1 x CA: CALCIUM ION(Non-covalent)

CA.3: 3 residues within 4Å: Chain A: V.122, D.123, E.305 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.123, A:E.305, A:E.305, H2O.2, H2O.2

1 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.4: 12 residues within 4Å: Chain A: F.161, E.163, K.178, Q.182, R.187, I.188, T.189 Chain B: R.229, L.230, L.342, H.345, P.346 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:E.163, A:R.187 Hydrogen bonds: A:R.187, A:I.188

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

PO4.6: 8 residues within 4Å: Chain B: N.127, K.130, L.131, E.134, D.195, F.242, C.243, S.244 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.127, B:L.131, B:D.195, B:F.242, B:S.244 Water bridges: B:S.244

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
C

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

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