MolNFT v1 · #125164 · protein
Human POGLUT1 in complex with 2F-glucose modified EGF(+) and udp
5L0V · Protein O-glucosyltransferase 1: “Human POGLUT1 in complex with 2F-glucose modified EGF(+) and udp”. X-ray diffraction, 4 ligands (UDP, SHG, NAG), 6 pockets (best druggability 0.84). MolNFT v1 #125164 on GenesisL1: 3D structure…
- PDB
- 5L0V
- Type
- protein
- Length
- 395 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein O-glucosyltransferase 1; EGF(+)
- EC
- 2.4.1.-, 2.4.2.26
- UniProt
- Q8NBL1
- Ligands
- UDP, SHG, NAG, CA
- Pockets
- 6 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein O-glucosyltransferase 1 (EC 2.4.1.-, 2.4.2.26) | protein | 356 | 42% helix, 16% strand | Q8NBL1 |
| B | EGF(+) | protein | 39 | 10% helix, 26% strand | — |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · chains A
- SHG · 2-deoxy-2-fluoro-beta-D-glucopyranose · ligand · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
- CA · Calcium ion · metal · chains B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 253 | 0.84 | 0.96 | 34 | UDP, SHG |
| 2 | 73 | 0.39 | 0.79 | 14 | empty |
| 3 | 78 | 0.37 | 0.77 | 22 | empty |
| 4 | 70 | 0.34 | 0.76 | 17 | empty |
| 5 | 55 | 0.29 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 843 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 4 glycan, 1 covalent (disulfide, N-glycosylation, covalent ligand).
Compared structures
- 5L0V · human POGLUT1 in complex with 2F-glucose modified EGF(+) and UDP · the same entry in another collection · chain A against A, TM-score 1.00
- Q8NBL1 · AlphaFold monomer V2.0 prediction for protein O-glucosyltransferase 1 (Q8NBL1) · a predicted model of the same protein · chain A against A, TM-score 1.00
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 Q8NBL1
- Elsewhere: RCSB PDB 5L0V · PDBe 5L0V · UniProt Q8NBL1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.