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Co-crystal structure of lenacapavir bound to N74D mutant of disulfide stabilized HIV-1 ca hexamer
Analyse Co-crystal structure of lenacapavir bound to N74D mutant of disulfide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RJ4
- Type
- protein
- Length
- 658 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein P24
- UniProt
- B6DRA0
- Ligands
- QNG, CL, IOD
- Pockets
- 5 · best druggability 0.35
Structure
x-ray diffraction · 3 distinct chains · 59% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein P24 | protein | 219 | 58% helix, 3% strand | B6DRA0 |
| B | Capsid protein P24 | protein | 219 | 60% helix, 3% strand | B6DRA0 |
| C | Capsid protein P24 | protein | 220 | 58% helix, 3% strand | B6DRA0 |
Ligands and binding sites
- QNG · N-[(1S)-1-(3-{4-chloro-3-[(methylsulfonyl)amino]-1-(2, 2,2-trifluoroethyl)-1H-indazol-7-yl}-6-[3-methyl-3-(methylsulfonyl)but-1-yn-1-yl]pyridin-2-yl)-2-(3,5-difluorophenyl)ethyl]-2-[(3bs,4ar)-5,5-difluoro-3-(trifluoromethyl)-3B,4,4A,5-tetrahydro-1H-cyclopropa[3,4]cyclopenta[1,2-c]pyrazol-1-yl]acetamide · ligand · 3 copies · chains A, B, C
- CL · Chloride ion · ion · 18 copies · chains A, B, C
- IOD · Iodide ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 87 | 0.35 | 0.75 | 17 | empty |
| 2 | 68 | 0.33 | 0.76 | 17 | empty |
| 3 | 63 | 0.33 | 0.76 | 13 | empty |
| 4 | 64 | 0.31 | 0.75 | 15 | empty |
| 5 | 50 | 0.28 | 0.75 | 14 | empty |
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7RJ4 · Co-crystal structure of lenacapavir bound to N74D mutant of disulfide stabilized HIV-1 CA… · 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 B6DRA0
- Elsewhere: RCSB PDB 7RJ4 · PDBe 7RJ4 · UniProt B6DRA0
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