SMTL ID : 6w2l.1

Crystal structure of human dehydrodolichyl diphosphate synthase (NgBR/DHDDS) in complex with Mg and IPP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.31 Å

Oligo State

hetero-1-1-mer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: D.34, R.85 Chain B: R.211 Ligands: IPE.2, IPE.3 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.34, H2O.1

2 x IPE: 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE(Non-covalent)

IPE.2: 12 residues within 4Å: Chain A: M.33, D.34, G.35, N.36, R.37, R.38, H.51, A.77, N.82, R.85 Ligands: MG.1, IPE.3 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.35, A:N.36, A:R.37, A:R.38 Salt bridges: A:R.37, A:R.37, A:R.38, A:H.51, A:R.85 Water bridges: B:R.211 IPE.3: 16 residues within 4Å: Chain A: I.32, M.33, D.34, Y.76, A.77, F.78, N.82, R.85, R.205, R.211, S.213 Chain B: R.211, L.212, G.213 Ligands: MG.1, IPE.2 18 PLIP interactions: 14 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:I.32, A:D.34, A:Y.76, A:Y.76 Hydrogen bonds: A:N.82, A:S.213, B:R.211, B:R.211, B:L.212, B:G.213 Water bridges: A:R.85, A:R.85, A:R.205, A:R.205 Salt bridges: A:R.85, A:R.205, A:R.205, A:R.211

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Edani, B.H. et al., Structural elucidation of thecis-prenyltransferase NgBR/DHDDS complex reveals insights in regulation of protein glycosylation. Proc.Natl.Acad.Sci.USA (2020)

Release Date

2020-08-19

Peptides

Dehydrodolichyl diphosphate synthase complex subunit DHDDS: A
Dehydrodolichyl diphosphate synthase complex subunit NUS1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dehydrodolichyl diphosphate synthase complex subunit DHDDS

Dehydrodolichyl diphosphate synthase complex subunit NUS1