Research workbench
Crystal structure of HIV-1 reverse transcriptase in complex with 4- ((6-cyanonaphthalen-1-YL)OXY)-3-(2-(2,4-dioxo-3,4-dihydropyrimidin- 1(2H)-YL)ETHOXY)PHENYL sulfurofluoridate (JLJ704)
Analyse Crystal structure of HIV-1 reverse transcriptase in complex with 4… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KRE
- Type
- protein
- Length
- 940 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, 2.7.7.7, 3.1.26.13
- UniProt
- P03366
- Ligands
- X2V
- Pockets
- 15 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HIV-1 reverse transcriptase, P66 subunit (EC 2.7.7.49, 2.7.7.7, 3.1.26.13) | protein | 534 | 31% helix, 24% strand | P03366 |
| B | HIV-1 reverse transcriptase, P51 subunit | protein | 406 | 38% helix, 20% strand | P03366 |
Ligands and binding sites
- X2V · 4-[(6-cyanonaphthalen-1-yl)oxy]-3-[2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy]phenyl sulfurofluoridate · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 853 | 0.79 | 0.81 | 84 | empty |
| 2 | 342 | 0.73 | 0.85 | 42 | X2V |
| 3 | 647 | 0.72 | 0.79 | 61 | empty |
| 4 | 303 | 0.67 | 0.82 | 40 | empty |
| 5 | 394 | 0.62 | 0.77 | 45 | empty |
Interfaces
1 interface between chains.
- A–B · 2367 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 7KRE · 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 7KRE · PDBe 7KRE · UniProt P03366
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