MolNFT v1 · #58187 · protein
Crystal structures of novel allosteric peptide inhibitors of HIV integrase in the ledgf binding site
3AVM: “Crystal structures of novel allosteric peptide inhibitors of HIV integrase in the ledgf binding site”. X-ray diffraction, 2 ligands (SO4, CL), 7 pockets (best druggability 0.65). MolNFT v1 #58187 on GenesisL1: 3D structure, binding…
- 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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