MolNFT v1 · #125160 · protein
Human POGLUT1 in complex with NOTCH1 EGF12 and udp
5L0R · Protein O-glucosyltransferase 1: “Human POGLUT1 in complex with NOTCH1 EGF12 and udp”. X-ray diffraction, 4 ligands (UDP, NAG, CA), 4 pockets (best druggability 0.84). MolNFT v1 #125160 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5L0R
- Type
- protein
- Length
- 394 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein O-glucosyltransferase 1; Neurogenic locus notch homolog protein 1
- EC
- 2.4.1.-, 2.4.2.26
- UniProt
- Q8NBL1, P46531
- Ligands
- UDP, NAG, CA, CL
- Pockets
- 4 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 39% 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 | 355 | 42% helix, 15% strand | Q8NBL1 |
| B | Neurogenic locus notch homolog protein 1 | protein | 39 | 10% helix, 36% strand | P46531 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- CA · Calcium ion · metal · chains B
- CL · Chloride ion · ion · chains A, B
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 241 | 0.84 | 0.96 | 37 | UDP, GOL |
| 2 | 68 | 0.40 | 0.80 | 17 | empty |
| 3 | 70 | 0.32 | 0.75 | 19 | empty |
| 4 | 51 | 0.26 | 0.73 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 889 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5L0R · human POGLUT1 in complex with Notch1 EGF12 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
- P46531 · AlphaFold monomer V2.0 prediction for neurogenic locus notch homolog protein 1 (P46531) · a predicted model of the same protein · chain B against A, TM-score 0.84
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
- Every structure of UniProt P46531
- Elsewhere: RCSB PDB 5L0R · PDBe 5L0R · UniProt Q8NBL1 · UniProt P46531
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