Research workbench
Crystal structure of HIV-1 reverse transcriptase (rt) in complex with (E)-3-(3-(2-(2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-YL)ETHOXY)- 4- fluorophenoxy)-5-FLUOROPHENYL)ACRYLONITRILE (JLJ506), a non- nucleoside inhibitor
Analyse Crystal structure of HIV-1 reverse transcriptase (rt) in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4H4O
- Type
- protein
- Length
- 977 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reverse TRANSCRIPTASE/RIBONUCLEASE H, exoribonuclease H, P66 rt; Reverse…
- EC
- 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.1.13.2
- UniProt
- P03366
- Ligands
- 506
- Pockets
- 19 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Reverse TRANSCRIPTASE/RIBONUCLEASE H, exoribonuclease H, P66 rt (EC 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.1.13.2) | protein | 549 | 31% helix, 22% strand | P03366 |
| B | Reverse TRANSCRIPTASE/RIBONUCLEASE H, exoribonuclease H, P51 rt (EC 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.1.13.2) | protein | 428 | 35% helix, 18% strand | P03366 |
Ligands and binding sites
- 506 · (2E)-3-(3-{2-[2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy]-4-fluorophenoxy}-5-fluorophenyl)prop-2-enenitrile · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 945 | 0.75 | 0.78 | 75 | empty |
| 2 | 332 | 0.73 | 0.85 | 39 | 506 |
| 3 | 658 | 0.72 | 0.79 | 57 | empty |
| 4 | 340 | 0.70 | 0.83 | 40 | empty |
| 5 | 286 | 0.67 | 0.82 | 38 | empty |
Interfaces
1 interface between chains.
- A–B · 2544 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 4H4O · Crystal Structure of HIV-1 Reverse Transcriptase (RT) 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 4H4O · PDBe 4H4O · UniProt P03366
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