Research workbench
X-ray crystal structure of wild type HIV-1 protease in complex with GRL-001
Analyse X-ray crystal structure of wild type HIV-1 protease in complex with GRL-001 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MCR
- Type
- protein
- Length
- 99 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.48
- Source
- Human immunodeficiency virus 1
- Molecule
- Protease
- UniProt
- Q8ULI2
- Ligands
- JDY
- Pockets
- 2 · best druggability 0.46
Structure
x-ray diffraction · resolution 1.48 · 1 distinct chain · 7% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protease | protein | 99 | 7% helix, 48% strand | Q8ULI2 |
Ligands and binding sites
- JDY · (3S,3aR,5R,7aS,8S)-hexahydro-4H-3,5-methanofuro[2,3-b]pyran-8-yl [(2S,3R)-4-[{[2-(cyclopropylamino)-1,3-benzothiazol-6-yl]sulfonyl}(2-methylpropyl)amino]-1-(3-fluorophenyl)-3-hydroxybutan-2-yl]carbamate · ligand · chains A
- EDO · 1,2-ethanediol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 148 | 0.46 | 0.76 | 20 | empty |
| 2 | 71 | 0.30 | 0.73 | 18 | empty |
Compared structures
- 6MCR · X-ray crystal structure of wild type HIV-1 protease in complex with grl-001 · 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 Q8ULI2
- Elsewhere: RCSB PDB 6MCR · PDBe 6MCR · UniProt Q8ULI2
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