MolNFT v1 · #137062 · protein
Alpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase with bound udp and manganese
5VCM · Alpha-1,6-mannosyl-glycoprotein 2-beta-N…: “Alpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase with bound udp and manganese”. X-ray diffraction, 3 ligands (UDP, NAG, MN), 8 pockets (best druggability 0.85).…
- PDB
- 5VCM
- Type
- protein
- Length
- 709 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
- UDP, NAG, MN
- Pockets
- 8 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 17% 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 | 351 | 38% helix, 17% strand | Q10469 |
| B | Alpha-1,6-mannosyl-glycoprotein 2-beta-N- acetylglucosaminyltransferase (EC 2.4.1.143) | protein | 358 | 37% helix, 17% strand | Q10469 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 8 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1139 | 0.85 | 0.86 | 111 | MN, UDP |
| 2 | 157 | 0.54 | 0.81 | 24 | MN, DMS |
| 3 | 128 | 0.51 | 0.80 | 18 | empty |
| 4 | 57 | 0.44 | 0.83 | 19 | empty |
| 5 | 60 | 0.35 | 0.78 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1677 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 5VCM · Alpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase with bound UDP and… · 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 A 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 5VCM · PDBe 5VCM · UniProt Q10469
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