MolNFT v1 · #137068 · protein
Alpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase with bound acceptor
5VCS · Alpha-1,6-mannosyl-glycoprotein 2-beta-N…: “Alpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase with bound acceptor”. X-ray diffraction, 3 ligands (NAG, MAN, BMA), 9 pockets (best druggability 0.81). MolNFT v1…
- PDB
- 5VCS
- Type
- protein
- Length
- 677 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-1,6-mannosyl-glycoprotein 2-beta-N- acetylglucosaminyltransferase
- EC
- 2.4.1.143
- UniProt
- Q10469
- Ligands
- NAG, MAN, BMA
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-1,6-mannosyl-glycoprotein 2-beta-N- acetylglucosaminyltransferase (EC 2.4.1.143) | protein | 354 | 39% helix, 15% strand | Q10469 |
| B | Alpha-1,6-mannosyl-glycoprotein 2-beta-N- acetylglucosaminyltransferase (EC 2.4.1.143) | protein | 323 | 37% helix, 18% strand | Q10469 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 3 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 171 | 0.81 | 0.96 | 24 | empty |
| 2 | 375 | 0.65 | 0.79 | 34 | DMS |
| 3 | 114 | 0.50 | 0.80 | 26 | empty |
| 4 | 99 | 0.49 | 0.81 | 24 | empty |
| 5 | 175 | 0.47 | 0.76 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1417 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 3 glycan (disulfide, N-glycosylation, glycosylation).
Compared structures
- 5VCS · Alpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase with Bound Acceptor · the same entry in another collection · chain A against A, TM-score 1.00
- Q10469 · AlphaFold monomer V2.0 prediction for alpha-1,6-mannosyl-glycoprotein… · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q10469
- Elsewhere: RCSB PDB 5VCS · PDBe 5VCS · UniProt Q10469
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