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Crystal structures of novel allosteric peptide inhibitors of HIV integrase in the ledgf binding site
Analyse Crystal structures of novel allosteric peptide inhibitors of HIV integrase in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3AVM
- Type
- protein
- Length
- 314 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrase; Ledgf peptide
- UniProt
- P12497
- Ligands
- SO4, CL
- Pockets
- 7 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Integrase | protein | 149 | 52% helix, 20% strand | P12497 |
| D, F | Ledgf peptide | protein | 8 | 0% helix, 25% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 8 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- ACY · Acetic acid · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 236 | 0.65 | 0.83 | 30 | SO4, ACY |
| 2 | 104 | 0.50 | 0.82 | 26 | ACY |
| 3 | 112 | 0.48 | 0.80 | 25 | ACY |
| 4 | 152 | 0.45 | 0.76 | 29 | empty |
| 5 | 55 | 0.44 | 0.84 | 13 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1492 Ų buried · 17 hydrogen bonds · protein-protein
- A–F · 250 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 245 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 215 Ų buried · 1 hydrogen bond · protein-protein
- B–F · 214 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3AVM · Crystal structures of novel allosteric peptide inhibitors of HIV integrase in the LEDGF… · the same entry in another collection · 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 P12497
- Elsewhere: RCSB PDB 3AVM · PDBe 3AVM · UniProt P12497
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