Research workbench
HIV integrase binding domain of lens epithelium-derived growth factor
Analyse HIV integrase binding domain of lens epithelium-derived growth factor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OYM
- Type
- protein
- Length
- 687 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PC4 and SFRS1-interacting protein
- UniProt
- O75475
- Pockets
- 8 · best druggability 0.53
Structure
x-ray diffraction · 5 distinct chains · 73% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H, A, C | PC4 and SFRS1-interacting protein | protein | 85 | 71% helix, 5% strand | O75475 |
| G | PC4 and SFRS1-interacting protein | protein | 88 | 78% helix, 0% strand | O75475 |
| B | PC4 and SFRS1-interacting protein | protein | 84 | 71% helix, 5% strand | O75475 |
| D, F | PC4 and SFRS1-interacting protein | protein | 87 | 74% helix, 0% strand | O75475 |
| E | PC4 and SFRS1-interacting protein | protein | 86 | 71% helix, 5% strand | O75475 |
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 200 | 0.53 | 0.78 | 39 | empty |
| 2 | 182 | 0.52 | 0.78 | 34 | empty |
| 3 | 146 | 0.41 | 0.74 | 26 | empty |
| 4 | 60 | 0.41 | 0.81 | 15 | empty |
| 5 | 126 | 0.40 | 0.75 | 20 | empty |
Interfaces
12 interfaces between chains.
- E–F · 2313 Ų buried · 5 hydrogen bonds · protein-protein
- H–G · 2295 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 2247 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 2223 Ų buried · 5 hydrogen bonds · protein-protein
- A–E · 528 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5OYM · HIV Integrase Binding Domain of Lens Epithelium-Derived Growth Factor · the same entry in another collection · chain F against F, TM-score 1.00
- O75475 · AlphaFold monomer V2.0 prediction for PC4 and SFRS1-interacting protein (O75475) · a predicted model of the same protein · chain B against A, TM-score 0.70
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 O75475
- Elsewhere: RCSB PDB 5OYM · PDBe 5OYM · UniProt O75475
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