Research workbench
Crystal structure of HIV-1 reverse transcriptase in complex with (E)- 3-(3-bromo-5-(4-chloro-2-(2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)- YL)ETHOXY)PHENOXY)PHENYL)ACRYLONITRILE (JLJ518), a non-nucleoside inhibitor
Analyse Crystal structure of HIV-1 reverse transcriptase in complex with (E)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LSN
- Type
- protein
- Length
- 965 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV-1 reverse transcriptase, P66 subunit; HIV-1 reverse transcriptase, P51 subunit
- EC
- 2.7.7.49
- UniProt
- P03366
- Ligands
- 1YR
- Pockets
- 16 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HIV-1 reverse transcriptase, P66 subunit (EC 2.7.7.49) | protein | 549 | 30% helix, 24% strand | P03366 |
| B | HIV-1 reverse transcriptase, P51 subunit (EC 2.7.7.49) | protein | 416 | 33% helix, 18% strand | P03366 |
Ligands and binding sites
- 1YR · (2E)-3-(3-bromo-5-{4-chloro-2-[2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy]phenoxy}phenyl)prop-2-enenitrile · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1003 | 0.81 | 0.82 | 109 | empty |
| 2 | 277 | 0.74 | 0.87 | 38 | 1YR |
| 3 | 489 | 0.72 | 0.81 | 48 | empty |
| 4 | 297 | 0.67 | 0.82 | 38 | empty |
| 5 | 440 | 0.63 | 0.77 | 37 | empty |
Interfaces
1 interface between chains.
- A–B · 2655 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 4LSN · Crystal Structure of HIV-1 Reverse Transcriptase in Complex with… · 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 4LSN · PDBe 4LSN · UniProt P03366
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