MolNFT v2 · #221792 · protein
Crystal Structure of HIV-1 Reverse Transcriptase in Complex with N-(2-(5-chloro-2-((2-cyanoindolizin-8-yl)oxy)phenoxy)ethyl)-N-methylacrylamide (JLJ746), a non-nucleoside inhibitor
8U6J · Reverse transcriptase/ribonuclease H: “Crystal Structure of HIV-1 Reverse Transcriptase in Complex with…”. X-ray diffraction at 2.64, 2 ligands (VR9, MG), 17 pockets (best druggability 0.72). MolNFT v2 #221792 on GenesisL1: 3D…
- PDB
- 8U6J
- Type
- protein
- Length
- 951 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.64
- Source
- Human immunodeficiency virus 1
- Molecule
- Reverse transcriptase/ribonuclease H; p51 RT
- EC
- 2.7.7.49, 2.7.7.7, 3.1.26.13
- UniProt
- P03366
- Ligands
- VR9, MG
- Pockets
- 17 · best druggability 0.72
Structure
x-ray diffraction · resolution 2.64 · 2 distinct chains · 33% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Reverse transcriptase/ribonuclease H (EC 2.7.7.49, 2.7.7.7, 3.1.26.13) | protein | 543 | 32% helix, 24% strand | P03366 |
| B | p51 RT | protein | 408 | 35% helix, 17% strand | P03366 |
Ligands and binding sites
- VR9 · N-[2-(5-chloro-2-{[(4R)-2-cyanoindolizin-8-yl]oxy}phenoxy)ethyl]-N-methylpropanamide · ligand · chains A
- MG · Magnesium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 677 | 0.72 | 0.79 | 75 | VR9 |
| 2 | 720 | 0.71 | 0.78 | 54 | empty |
| 3 | 306 | 0.67 | 0.81 | 42 | empty |
| 4 | 228 | 0.65 | 0.83 | 40 | empty |
| 5 | 78 | 0.61 | 0.90 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 2450 Ų buried · 24 hydrogen bonds · protein-protein
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 8U6J · PDBe 8U6J · UniProt P03366
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