Research workbench
Structure of S. cerevisiae protein O-mannosyltransferase PMT1-PMT2 complex bound to the sugar donor and a peptide acceptor
Analyse Structure of S. cerevisiae protein O-mannosyltransferase PMT1-PMT2 complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6P25
- Type
- protein
- Length
- 1,424 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dolichyl-phosphate-mannose--protein mannosyltransferase 1…
- EC
- 2.4.1.109
- UniProt
- P33775, P31382
- Ligands
- CPL, NNM, NAG
- Pockets
- 13 · best druggability 0.75
Structure
electron microscopy · 3 distinct chains · 46% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dolichyl-phosphate-mannose--protein mannosyltransferase 1 (EC 2.4.1.109) | protein | 731 | 45% helix, 14% strand | P33775 |
| B | Dolichyl-phosphate-mannose--protein mannosyltransferase 2 (EC 2.4.1.109) | protein | 690 | 47% helix, 13% strand | P31382 |
| D | Acceptor peptide | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- CPL · 1-palmitoyl-2-linoleoyl-sn-glycero-3-phosphocholine · ligand · 3 copies · chains A, B
- NNM · (3R)-3,31-dimethyl-7,11,15,19,23,27-hexamethylidenedotriacont-31-en-1-yl dihydrogen phosphate · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 536 | 0.75 | 0.83 | 45 | empty |
| 2 | 592 | 0.67 | 0.76 | 69 | empty |
| 3 | 475 | 0.65 | 0.77 | 52 | empty |
| 4 | 168 | 0.64 | 0.85 | 25 | empty |
| 5 | 333 | 0.60 | 0.77 | 50 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1115 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 319 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 glycan, 1 disulfide (N-glycosylation, disulfide).
Compared structures
- 6P25 · Structure of S. cerevisiae protein O-mannosyltransferase Pmt1-Pmt2 complex bound to the… · the same entry in another collection · chain A against A, TM-score 1.00
- P33775 · AlphaFold monomer V2.0 prediction for dolichyl-phosphate-mannose-- protein… · a predicted model of the same protein · chain A against A, TM-score 0.97
- P31382 · AlphaFold monomer V2.0 prediction for dolichyl-phosphate-mannose-- protein… · a predicted model of the same protein · chain B against A, TM-score 0.94
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P33775
- Every structure of UniProt P31382
- Elsewhere: RCSB PDB 6P25 · PDBe 6P25 · UniProt P33775 · UniProt P31382
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