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The crystallographic structure of the protease from human immunodeficiency virus type 2 with two synthetic peptidic transition state analog inhibitors
Analyse The crystallographic structure of the protease from human immunodeficiency… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1IVP
- Type
- protein
- Length
- 198 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV-2 protease
- UniProt
- P04584
- Ligands
- 1ZK
- Pockets
- 1 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 7% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | HIV-2 protease | protein | 99 | 7% helix, 54% strand | P04584 |
Ligands and binding sites
- 1ZK · 4-[(2R)-3-{[(1S,2S,3R,4S)-1-(cyclohexylmethyl)-2,3-dihydroxy-5-methyl-4-({(1S,2R)-2-methyl-1-[(pyridin-2-ylmethyl)carba moyl]butyl}carbamoyl)hexyl]amino}-2-{[(naphthalen-1-yloxy)acetyl]amino}-3-oxopropyl]-1H-imidazol-3-ium · ligand · 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 | 402 | 0.70 | 0.82 | 35 | 1ZK |
Interfaces
1 interface between chains.
- A–B · 1742 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 1IVP · The crystallographic structure of the protease from human immunodeficiency virus type 2… · 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 P04584
- Elsewhere: RCSB PDB 1IVP · PDBe 1IVP · UniProt P04584
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