MolNFT v1 · #118640 · protein
Crystal structure of drosophila POGLUT1 (rumi) complexed with udp
5F87 · O-glucosyltransferase rumi: “Crystal structure of drosophila POGLUT1 (rumi) complexed with udp”. X-ray diffraction, 1 ligand (UDP), 20 pockets (best druggability 0.83). MolNFT v1 #118640 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5F87
- Type
- protein
- Length
- 2,190 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- O-glucosyltransferase rumi
- EC
- 2.4.1.-
- UniProt
- Q8T045
- Ligands
- UDP
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | O-glucosyltransferase rumi (EC 2.4.1.-) | protein | 365 | 41% helix, 16% strand | Q8T045 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 6 copies · chains A, B, C, D, E, F
- GOL · Glycerol · additive · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 983 | 0.83 | 0.84 | 82 | UDP, GOL |
| 2 | 477 | 0.77 | 0.85 | 52 | UDP, GOL |
| 3 | 337 | 0.76 | 0.87 | 36 | UDP, GOL |
| 4 | 438 | 0.74 | 0.84 | 39 | UDP, GOL |
| 5 | 387 | 0.74 | 0.84 | 38 | UDP, GOL |
Interfaces
5 interfaces between chains.
- A–B · 1211 Ų buried · 18 hydrogen bonds · protein-protein
- D–E · 1177 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 658 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 570 Ų buried · 4 hydrogen bonds · protein-protein
- C–F · 404 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide (disulfide).
Compared structures
- 5F87 · Crystal structure of Drosophila Poglut1 (Rumi) complexed with UDP · the same entry in another collection · chain C against C, TM-score 1.00
- Q8T045 · AlphaFold monomer V2.0 prediction for O-glucosyltransferase rumi (Q8T045) · 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 Q8T045
- Elsewhere: RCSB PDB 5F87 · PDBe 5F87 · UniProt Q8T045
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