SMTL ID : 6p2r.1

Structure of S. cerevisiae protein O-mannosyltransferase Pmt1-Pmt2 complex bound to the sugar donor

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.1: 4 residues within 4Å: Chain A: F.388, N.390, V.456, R.460 No protein-ligand interaction detected (PLIP) NAG.4: 3 residues within 4Å: Chain B: N.131, S.133, Y.145 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.131, B:S.133

3 x CPL: 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

CPL.2: 13 residues within 4Å: Chain A: T.562, F.566, T.594, I.597, G.598, I.599, I.631, L.634, F.637, A.638, Y.641, A.642, F.645 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.566, A:I.599, A:I.631, A:L.634, A:L.634, A:F.637, A:A.638, A:Y.641, A:A.642 CPL.5: 14 residues within 4Å: Chain A: I.256, L.259, S.263, I.266, F.267, A.270, F.271 Chain B: V.626, I.627, I.630, R.631, R.634, Y.636 Ligands: NNM.3 14 PLIP interactions: 6 interactions with chain A, 8 interactions with chain B Hydrophobic interactions: A:I.256, A:I.256, A:I.266, A:F.267, A:A.270, A:F.271, B:V.626, B:I.627, B:I.630, B:I.630, B:R.631 Salt bridges: B:R.634, B:R.634 pi-Cation interactions: B:Y.636 CPL.6: 18 residues within 4Å: Chain B: A.613, V.616, L.619, A.620, A.623, T.624, I.627, L.628, R.631, D.638, R.640, L.689, Y.691, C.692, F.693, A.695, G.696, K.699 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:A.613, B:V.616, B:L.619, B:A.620, B:I.627, B:L.628, B:L.628, B:Y.691, B:F.693, B:A.695 Hydrogen bonds: B:K.699, B:K.699 Salt bridges: B:R.631, B:K.699

1 x NNM: (3R)-3,31-dimethyl-7,11,15,19,23,27-hexamethylidenedotriacont-31-en-1-yl dihydrogen phosphate(Non-covalent)

NNM.3: 19 residues within 4Å: Chain A: H.98, K.234, W.235, L.238, F.239, T.242, G.245, C.248, L.252, L.274, L.277, L.278, W.545, N.548, M.647, R.649, H.654, H.655 Ligands: CPL.5 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:W.235, A:W.235, A:L.238, A:F.239, A:F.239, A:L.252, A:L.277, A:L.278, A:L.278, A:L.278 Salt bridges: A:H.98, A:K.234, A:R.649, A:H.654, A:H.655

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bai, L. et al., Structure of the eukaryotic protein O-mannosyltransferase Pmt1-Pmt2 complex. Nat.Struct.Mol.Biol. (2019)

Release Date

2019-07-10

Peptides

Dolichyl-phosphate-mannose--protein mannosyltransferase 1: A
Dolichyl-phosphate-mannose--protein mannosyltransferase 2: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

We predict this structure to be a membrane protein.
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Dolichyl-phosphate-mannose--protein mannosyltransferase 1

Dolichyl-phosphate-mannose--protein mannosyltransferase 2

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