SMTL ID : 5mm0.1

Dolichyl phosphate mannose synthase in complex with GDP-mannose and Mn2+ (donor complex)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

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

GDD.1: 24 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, F.199, K.200, F.221, R.224, S.229, K.230 Ligands: MN.2 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:T.31, A:Y.32, A:Y.32, A:E.34, A:V.59, A:D.61, A:G.90, A:G.90, A:D.111, A:A.112, A:R.139, A:V.178, A:G.180, A:K.200, A:K.230, A:L.231 Water bridges: A:R.139 Salt bridges: A:D.61, A:R.224, A:K.230

1 x MN: MANGANESE (II) ION(Non-covalent)

MN.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 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

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

LDA.4: 6 residues within 4Å: Chain A: S.265, L.268, W.302, I.305, W.306 Ligands: LDA.7 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.302, A:W.302, A:W.306, A:W.306, A:W.306 LDA.5: 3 residues within 4Å: Chain A: G.272, F.273, W.275 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.273, A:W.275, A:W.275, A:W.275 LDA.6: 1 residues within 4Å: Chain A: W.339 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.339, A:W.339 LDA.7: 2 residues within 4Å: Chain A: W.306 Ligands: LDA.4 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.306 LDA.8: 7 residues within 4Å: Chain A: G.266, I.267, N.270, V.292, S.295, N.299, L.328 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.292 Hydrogen bonds: A:N.299 Water bridges: A:I.267

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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