MolNFT v1 · #159844 · protein
Structure of S. cerevisiae protein O-mannosyltransferase PMT1-PMT2 complex bound to the sugar donor
6P2R · Dolichyl-phosphate-mannose--protein mannosyltransferase 1: “Structure of S. cerevisiae protein O-mannosyltransferase PMT1-PMT2 complex bound to the sugar donor”. Electron microscopy, 3 ligands (CPL, NNM, NAG), 14 pockets (best…
- PDB
- 6P2R
- Type
- protein
- Length
- 1,421 residues
- Chains
- 2
- 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
- 14 · best druggability 0.75
Structure
electron microscopy · 2 distinct chains · 45% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dolichyl-phosphate-mannose--protein mannosyltransferase 1 (EC 2.4.1.109) | protein | 731 | 44% helix, 14% strand | P33775 |
| B | Dolichyl-phosphate-mannose--protein mannosyltransferase 2 (EC 2.4.1.109) | protein | 690 | 47% helix, 11% strand | P31382 |
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
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 516 | 0.75 | 0.82 | 47 | empty |
| 2 | 351 | 0.68 | 0.81 | 41 | NNM |
| 3 | 447 | 0.64 | 0.77 | 55 | empty |
| 4 | 327 | 0.61 | 0.78 | 48 | empty |
| 5 | 427 | 0.58 | 0.74 | 47 | empty |
Interfaces
1 interface between chains.
- A–B · 1091 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 glycan, 1 disulfide (N-glycosylation, disulfide).
Compared structures
- 6P2R · 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 6P2R · PDBe 6P2R · UniProt P33775 · UniProt P31382
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