Research workbench
Crystal structure of HIV-1 reverse transcriptase (Y181C) variant in complex with (E)-3-(3-chloro-5-(2-(2-(2,4-dioxo-3,4-dihydropyrimidin- 1(2H)-YL)ETHOXY)PHENOXY)PHENYL)ACRYLONITRILE (JLJ532), a non- nucleoside inhibitor
Analyse Crystal structure of HIV-1 reverse transcriptase (Y181C) variant in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RW9
- Type
- protein
- Length
- 943 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reverse TRANSCRIPTASE/RIBONUCLEASE H, P66 subunit; Reverse TRANSCRIPTASE/RIBONUCLEASE H…
- EC
- 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.1.13.2
- UniProt
- P03366
- Ligands
- 3X6
- Pockets
- 18 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Reverse TRANSCRIPTASE/RIBONUCLEASE H, P66 subunit (EC 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.1.13.2) | protein | 538 | 32% helix, 24% strand | P03366 |
| B | Reverse TRANSCRIPTASE/RIBONUCLEASE H, P51 subunit (EC 2.7.7.49) | protein | 405 | 34% helix, 21% strand | P03366 |
Ligands and binding sites
- 3X6 · (2E)-3-(3-chloro-5-{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
18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 586 | 0.77 | 0.83 | 46 | empty |
| 2 | 885 | 0.73 | 0.77 | 61 | empty |
| 3 | 210 | 0.72 | 0.88 | 31 | 3X6 |
| 4 | 603 | 0.68 | 0.77 | 48 | empty |
| 5 | 379 | 0.66 | 0.79 | 47 | empty |
Interfaces
1 interface between chains.
- A–B · 2673 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 4RW9 · Crystal Structure of HIV-1 Reverse Transcriptase (Y181C) variant 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 4RW9 · PDBe 4RW9 · UniProt P03366
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