SMTL ID : 5mlz.1

Dolichyl phosphate mannose synthase in complex with GDP and Mg2+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.1: 18 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, R.224, S.229, K.230, L.231 Ligands: MG.2 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:P.30, A:T.31, A:Y.32, A:E.34, A:V.59, A:G.90, A:A.112, A:Q.115, A:K.230, A:L.231 Salt bridges: A:D.61, A:R.224, A:K.230

1 x MG: MAGNESIUM ION(Non-covalent)

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

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 4 residues within 4Å: Chain A: F.259, N.299, F.323, R.363 Ligand excluded by PLIP

7 x LDA: LAURYL DIMETHYLAMINE-N-OXIDE(Non-covalent)

LDA.4: 4 residues within 4Å: Chain A: S.265, W.302, W.306 Ligands: LDA.7 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.302, A:W.302, A:W.306, A:W.306, A:W.306, A:W.306 LDA.5: 3 residues within 4Å: Chain A: G.272, F.273, W.275 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.273, A:W.275, A:W.275 LDA.6: 1 residues within 4Å: Chain A: W.339 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.339, A:W.339, A:W.339, A:W.339 LDA.7: 3 residues within 4Å: Chain A: I.261, W.306 Ligands: LDA.4 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.261, A:W.306 LDA.8: 9 residues within 4Å: Chain A: G.266, I.267, N.270, V.292, S.295, N.299, L.328, A.331 Ligands: LDA.9 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.292, A:A.331 Water bridges: A:I.267 LDA.9: 4 residues within 4Å: Chain A: I.289, V.292, E.293 Ligands: LDA.8 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.292 LDA.10: 3 residues within 4Å: Chain A: L.240, R.241, Y.244 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.244 Hydrogen bonds: A:Y.244

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gandini, R. et al., Structural basis for dolichylphosphate mannose biosynthesis. Nat Commun (2017)

Release Date

2017-08-09

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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