Research workbench
HIV-1 wild Type protease with GRL-0648A (a isophthalamide-derived P2-Ligand)
Analyse HIV-1 wild Type protease with GRL-0648A (a isophthalamide-derived P2-Ligand) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZIP
- Type
- protein
- Length
- 198 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.11
- Source
- Human immunodeficiency virus type 1
- Molecule
- Protease
- EC
- 3.4.23.16
- UniProt
- P03366
- Ligands
- G64, NA, CL
- Pockets
- 1 · best druggability 0.71
Structure
x-ray diffraction · resolution 1.11 · 1 distinct chain · 7% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Protease (EC 3.4.23.16) | protein | 99 | 7% helix, 56% strand | P03366 |
Ligands and binding sites
- G64 · N-[(2,5-dimethyl-1,3-oxazol-4-yl)methyl]-N'-[(2S,3R)-3-hydroxy-4-{[(4-methoxyphenyl)sulfonyl](2-methylpropyl)amino}-1-phenylbutan-2-yl]-N,5-dimethylbenzene-1,3-dicarboxamide · ligand · chains A, B
- NA · Sodium ion · metal · 3 copies · chains A, B
- CL · Chloride ion · ion · 3 copies · chains A, B
- GOL · Glycerol · additive · 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 | 404 | 0.71 | 0.82 | 41 | G64 |
Interfaces
1 interface between chains.
- A–B · 1866 Ų buried · 38 hydrogen bonds · protein-protein
Compared structures
- 4ZIP · HIV-1 wild type protease with grl-0648A (a isophthalamide-derived P2- ligand) · 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 P03366
- Elsewhere: RCSB PDB 4ZIP · PDBe 4ZIP · UniProt P03366
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