Research workbench
Mdr 769 HIV-1 protease in complex with reduced P1F
Analyse Mdr 769 HIV-1 protease in complex with reduced P1F in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GYE
- Type
- protein
- Length
- 203 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV-1 protease; P1F peptide
- EC
- 3.4.23.16
- UniProt
- Q9QM22
- Ligands
- PUK
- Pockets
- 1 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | HIV-1 protease (EC 3.4.23.16) | protein | 99 | 4% helix, 54% strand | Q9QM22 |
| C | P1F peptide | protein | 5 | 0% helix, 20% strand | — |
Ligands and binding sites
- PUK · N-[(2S)-2-amino-3-phenylpropyl]-L-phenylalanine · ligand · chains A, B, C
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 | 139 | 0.66 | 0.88 | 33 | PUK |
Interfaces
3 interfaces between chains.
- A–B · 1886 Ų buried · 34 hydrogen bonds · protein-protein
- B–C · 399 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 332 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 modified (covalent ligand, nonstandard).
Compared structures
- 4GYE · MDR 769 HIV-1 Protease in Complex with Reduced P1F · 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 Q9QM22
- Elsewhere: RCSB PDB 4GYE · PDBe 4GYE · UniProt Q9QM22
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