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Cystal structure of HIV-1 active site mutant D25N and P2-nc analog inhibitor
Analyse Cystal structure of HIV-1 active site mutant D25N and P2-nc analog inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BVA
- Type
- protein
- Length
- 198 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protease (retropepsin)
- EC
- 3.4.23.16
- UniProt
- P03367
- Ligands
- 2NC
- Pockets
- 1 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 4% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Protease (retropepsin) (EC 3.4.23.16) | protein | 99 | 4% helix, 55% strand | P03367 |
Ligands and binding sites
- 2NC · N-{(2S)-2-[(N-acetyl-L-threonyl-L-isoleucyl)amino]hexyl}-L-norleucyl-L-glutaminyl-N~5~-[amino(iminio)methyl]-L-ornithinamide · ligand · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 383 | 0.72 | 0.83 | 44 | 2NC |
Interfaces
1 interface between chains.
- A–B · 1848 Ų buried · 36 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (additive adduct).
Compared structures
- 3BVA · Cystal structure of HIV-1 Active Site Mutant D25N and p2-NC analog inhibitor · the same entry in another collection · chain B against B, 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 P03367
- Elsewhere: RCSB PDB 3BVA · PDBe 3BVA · UniProt P03367
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