SMTL ID : 9ep0.1

Dolichyl phosphate mannose synthase in complex with donor (GDP-Man) and traces of acceptor (Dol55P) and product (Dol55P-Man)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

monomer

Ligands

1 x GDD: GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE(Non-covalent)

GDD.1: 22 residues within 4Å: Chain A: P.30, T.31, Y.32, E.34, V.59, D.61, G.90, L.91, A.94, D.111, A.112, D.113, Q.115, H.116, R.139, V.178, G.180, K.200, F.221, R.224 Ligands: MG.2, EFS.3 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:Y.32, A:Y.32, A:V.59, A:D.61, A:G.90, A:A.112, A:R.139, A:G.180, A:K.200 Salt bridges: A:D.61, A:K.200, A:R.224

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.113, Q.115, R.224 Ligands: GDD.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.113

1 x EFS: ETHYL DIHYDROGEN PHOSPHATE(Non-covalent)

EFS.3: 7 residues within 4Å: Chain A: R.139, W.149, S.157, V.178, K.200, Y.239 Ligands: GDD.1 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.239 Hydrogen bonds: A:S.157 Salt bridges: A:R.139, A:K.200

1 x MJC: dolichyl phosphate mannose(Non-covalent)

MJC.4: 18 residues within 4Å: Chain A: V.163, I.166, A.167, I.256, S.260, G.263, L.264, G.266, I.267, N.270, V.292, S.295, N.299, V.357, F.360, G.361, R.363, Y.364 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:V.163, A:I.166, A:A.167, A:I.256, A:L.264, A:V.357, A:F.360, A:F.360, A:F.360, A:Y.364 Hydrogen bonds: A:G.263, A:N.270, A:S.295, A:S.295, A:N.299 Salt bridges: A:R.363, A:R.363

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gandini, R. et al., Crystal structure of Pyrococcus furiosus dolichylphosphate mannose synthase in complex with substrates (GDP-Man and DolP) and traces of a flipped glycolipid product (DolP-Man). To be published

Release Date

2025-10-01

Peptides

Dolichol monophosphate mannose synthase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

We predict this structure to be a membrane protein.
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Dolichol monophosphate mannose synthase

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