Research workbench
Crystal structure of drosophila POGLUT1 (rumi) complexed with its glycoprotein product (glucosylated EGF repeat) and udp
Analyse Crystal structure of drosophila POGLUT1 (rumi) complexed with its glycoprotein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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