Research workbench
Crystal structure of HIV-1 reverse transcriptase in complex with 5- chloro-7-(2-(2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-YL)ETHOXY) phenoxy)-8-methyl-2-naphthonitrile (JLJ651), a non-nucleoside inhibitor
Analyse Crystal structure of HIV-1 reverse transcriptase in complex with 5… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TER
- Type
- protein
- Length
- 948 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
- 3.4.23.16, 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.1.13.2, 2.7.7.-, 3.1.-.-
- UniProt
- P03366
- Ligands
- 7AY, MG, SO4
- Pockets
- 14 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HIV-1 reverse transcriptase, P66 subunit (EC 3.4.23.16, 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.1.13.2, 2.7.7.-, 3.1.-.-) | protein | 547 | 31% helix, 24% strand | P03366 |
| B | HIV-1 reverse transcriptase, P51 subunit (EC 3.4.23.16, 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.1.13.2, 2.7.7.-, 3.1.-.-) | protein | 401 | 35% helix, 20% strand | P03366 |
Ligands and binding sites
- 7AY · 5-chloro-7-(2-(2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy)phenoxy)-8-methyl-2-naphthonitrile · ligand · chains A
- MG · Magnesium ion · metal · chains A
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 725 | 0.78 | 0.82 | 59 | empty |
| 2 | 266 | 0.73 | 0.86 | 32 | 7AY |
| 3 | 444 | 0.70 | 0.81 | 52 | empty |
| 4 | 374 | 0.69 | 0.82 | 52 | empty |
| 5 | 547 | 0.68 | 0.78 | 48 | empty |
Interfaces
1 interface between chains.
- A–B · 2755 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 5TER · 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 5TER · PDBe 5TER · UniProt P03366
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