MolNFT v1 · #137067 · protein
Alpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase with bound uranium dioxide
5VCR · Alpha-1,6-mannosyl-glycoprotein 2-beta-N…: “Alpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase with bound uranium dioxide”. X-ray diffraction, 3 ligands (IUM, NAG, CL), 9 pockets (best druggability 0.83). MolNFT…
- PDB
- 5VCR
- Type
- protein
- Length
- 693 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
- IUM, NAG, CL
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 15% 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 | 350 | 39% helix, 15% strand | Q10469 |
| B | Alpha-1,6-mannosyl-glycoprotein 2-beta-N- acetylglucosaminyltransferase (EC 2.4.1.143) | protein | 343 | 38% helix, 15% strand | Q10469 |
Ligands and binding sites
- IUM · Uranyl (VI) ion · ligand · 4 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- CL · Chloride ion · ion · 2 copies · chains A
- DMS · Dimethyl sulfoxide · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 202 | 0.83 | 0.97 | 25 | empty |
| 2 | 68 | 0.48 | 0.83 | 16 | empty |
| 3 | 154 | 0.46 | 0.76 | 25 | IUM |
| 4 | 154 | 0.45 | 0.76 | 25 | IUM |
| 5 | 55 | 0.42 | 0.82 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1213 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 5VCR · Alpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase with bound uranium… · 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 5VCR · PDBe 5VCR · UniProt Q10469
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