SMTL ID : 6p25.1

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

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

1 x PRO- TYR- THR: acceptor peptide(Non-covalent)

PRO-TYR-THR.1: 9 residues within 4Å: Chain B: W.91, D.92, H.95, S.138, L.576, R.591, L.592, C.593, Y.674 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.576 Hydrogen bonds: B:D.92, B:D.92, B:S.138, B:S.138, B:Y.674

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

NAG.2: 3 residues within 4Å: Chain A: F.388, N.390, R.460 No protein-ligand interaction detected (PLIP) NAG.5: 3 residues within 4Å: Chain B: N.131, S.133, Y.145 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.131

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

CPL.3: 16 residues within 4Å: Chain A: Q.560, T.562, P.565, F.566, T.594, I.597, G.598, I.599, F.600, I.631, L.634, F.637, A.638, Y.641, A.642, F.645 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:P.565, A:P.565, A:F.566, A:I.599, A:F.600, A:I.631, A:L.634, A:L.634, A:L.634, A:F.637, A:A.638, A:Y.641, A:F.645 CPL.6: 14 residues within 4Å: Chain A: I.249, I.256, L.259, S.263, I.266, F.267, A.270 Chain B: V.626, I.627, I.630, R.631, R.634, Q.635, Y.636 14 PLIP interactions: 7 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:V.626, B:I.627, B:I.630, B:R.631, A:I.249, A:I.256, A:I.256, A:I.266, A:F.267, A:F.267, A:A.270 Salt bridges: B:R.634, B:R.634 pi-Cation interactions: B:Y.636 CPL.7: 17 residues within 4Å: Chain B: A.613, V.616, A.617, L.619, A.620, A.623, T.624, I.627, L.628, R.631, D.638, R.640, L.689, Y.691, C.692, G.696, K.699 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:A.613, B:V.616, B:V.616, B:A.617, B:L.619, B:A.620, B:T.624, B:I.627, B:L.628, B:L.628, B:L.689, B:Y.691 Salt bridges: B:R.631, B:K.699, 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.4: 20 residues within 4Å: Chain A: H.98, K.234, W.235, L.238, F.239, V.241, T.242, G.245, L.252, A.270, K.273, L.274, L.277, L.278, W.545, N.548, M.647, R.649, H.654, H.655 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:W.235, A:L.238, A:L.238, A:F.239, A:F.239, A:V.241, A:T.242, A:L.252, A:A.270, A:K.273, A:L.274, A:L.277, A:L.278, A:W.545 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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