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Crystal structure of HIV-1 protease mutants D30N complexed with inhibitor grl-0519
Analyse Crystal structure of HIV-1 protease mutants D30N complexed with inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HDB
- Type
- protein
- Length
- 198 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV-1 protease
- EC
- 3.4.23.16
- UniProt
- P03367
- Ligands
- G52, NA, CL
- Pockets
- 1 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 7% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | HIV-1 protease (EC 3.4.23.16) | protein | 99 | 7% helix, 54% strand | P03367 |
Ligands and binding sites
- G52 · (3r,3as,3br,6as,7as)-octahydrodifuro[2,3-B:3',2'-d]furan-3-yl [(1S,2R)-1-benzyl-2-hydroxy-3-{[(4-methoxyphenyl)sulfonyl](2-methylpropyl) amino}propyl]carbamate · ligand · chains A, B
- NA · Sodium ion · metal · chains A
- CL · Chloride ion · ion · 2 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 | 394 | 0.72 | 0.83 | 37 | G52 |
Interfaces
1 interface between chains.
- A–B · 1874 Ų buried · 38 hydrogen bonds · protein-protein
Compared structures
- 4HDB · Crystal Structure of HIV-1 protease mutants D30N complexed with inhibitor GRL-0519 · 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 P03367
- Elsewhere: RCSB PDB 4HDB · PDBe 4HDB · UniProt P03367
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