SMTL ID : 6pyp.1

Binary Complex of Human Glycerol 3-Phosphate Dehydrogenase, R269A mutant

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

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

NAD.1: 21 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 21 PLIP interactions: 21 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:K.120, A:A.153 Water bridges: A:F.41, A:Y.63, A:H.95, A:S.154 pi-Stacking: A:W.14, A:W.14, A:F.41, A:F.41, A:F.97, A:F.97

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

PO4.2: 4 residues within 4Å: Chain A: K.240, S.248, S.249 Chain B: A.250 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.249, A:S.249, A:S.249 Water bridges: A:A.250 Salt bridges: A:K.240

1 x 3SY: 2,2-bis(hydroxymethyl)propane-1,3-diol(Non-covalent)

3SY.3: 9 residues within 4Å: Chain A: N.127, L.129, 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:D.195, A:D.195, A:S.244 Water bridges: A:K.130, A:F.242

1 x POP: PYROPHOSPHATE 2-(Non-covalent)

POP.4: 6 residues within 4Å: Chain B: G.12, N.13, W.14, G.15, Y.63, P.94 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.13, B:W.14, B:G.15 Water bridges: B:G.12

1 x K: POTASSIUM ION(Non-covalent)

K.5: 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.13

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mhashal, A.R. et al., Modeling the Role of a Flexible Loop and Active Site Side Chains in Hydride Transfer Catalyzed by Glycerol-3-phosphate Dehydrogenase. Acs Catalysis (2020)

Release Date

2020-07-08

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