MolNFT v1 · #118637 · protein
Crystal structure of drosophila POGLUT1 (rumi) complexed with its glycoprotein product (glucosylated EGF repeat) and udp
5F84 · O-glucosyltransferase rumi: “Crystal structure of drosophila POGLUT1 (rumi) complexed with its glycoprotein product (glucosylated EGF…”. X-ray diffraction, 3 ligands (UDP, BGC, SO4), 4 pockets (best druggability 0.79). MolNFT v1…
- PDB
- 5F84
- Type
- protein
- Length
- 404 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- O-glucosyltransferase rumi; Coagulation factor IX
- EC
- 2.4.1.-, 3.4.21.22
- UniProt
- Q8T045, P00740
- Ligands
- UDP, BGC, SO4
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | O-glucosyltransferase rumi (EC 2.4.1.-) | protein | 365 | 40% helix, 16% strand | Q8T045 |
| B | Coagulation factor IX (EC 3.4.21.22) | protein | 39 | 10% helix, 31% strand | P00740 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · chains A
- BGC · beta-D-glucopyranose · sugar · chains A, B
- SO4 · Sulfate ion · ion · 5 copies · chains A
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 | 361 | 0.79 | 0.88 | 49 | UDP, BGC |
| 2 | 160 | 0.49 | 0.77 | 26 | empty |
| 3 | 74 | 0.32 | 0.75 | 13 | empty |
| 4 | 81 | 0.31 | 0.73 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 902 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 1 glycan (disulfide, O-glycosylation).
Compared structures
- 5F84 · Crystal structure of Drosophila Poglut1 (Rumi) complexed with its glycoprotein product… · the same entry in another collection · chain A against A, 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
- P00740 · AlphaFold monomer V2.0 prediction for coagulation factor IX (P00740) · a predicted model of the same protein · chain B against A, TM-score 0.89
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
- Every structure of UniProt P00740
- Elsewhere: RCSB PDB 5F84 · PDBe 5F84 · UniProt Q8T045 · UniProt P00740
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