MolNFT v1 · #31734 · protein
Structural basis for the recognition between HIV-1 integrase and LEDGF/P75
2B4J · Integrase (in): “Structural basis for the recognition between HIV-1 integrase and LEDGF/P75”. X-ray diffraction, 1 ligand (PO4), 6 pockets (best druggability 0.54). MolNFT v1 #31734 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2B4J
- Type
- protein
- Length
- 444 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrase (in); PC4 and SFRS1 interacting protein
- UniProt
- P12497, O75475
- Ligands
- PO4
- Pockets
- 6 · best druggability 0.54
Structure
x-ray diffraction · 3 distinct chains · 58% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integrase (in) | protein | 135 | 53% helix, 22% strand | P12497 |
| B | Integrase (in) | protein | 145 | 54% helix, 22% strand | P12497 |
| C, D | PC4 and SFRS1 interacting protein | protein | 82 | 72% helix, 0% strand | O75475 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 74 | 0.54 | 0.86 | 14 | empty |
| 2 | 83 | 0.54 | 0.85 | 14 | empty |
| 3 | 132 | 0.49 | 0.79 | 21 | empty |
| 4 | 115 | 0.43 | 0.77 | 18 | empty |
| 5 | 78 | 0.41 | 0.79 | 23 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1494 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 393 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 380 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 336 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 316 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 2B4J · Structural basis for the recognition between HIV-1 integrase and LEDGF/p75 · the same entry in another collection · chain A against A, 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 C against A, TM-score 0.97
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 P12497
- Every structure of UniProt O75475
- Elsewhere: RCSB PDB 2B4J · PDBe 2B4J · UniProt P12497 · UniProt O75475
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