MolNFT v2 · #207790 · protein
HIV-1 reverse transcriptase/rilpivirine with bound fragment 2-amino-6-fluorobenzonitrile at the NNRTI adjacent site
8DXE · Reverse transcriptase/ribonuclease H: “HIV-1 reverse transcriptase/rilpivirine with bound fragment 2-amino-6-fluorobenzonitrile at the NNRTI…”. X-ray diffraction at 1.85, 4 ligands (0IF, T27, MG), 16 pockets (best druggability…
- PDB
- 8DXE
- Type
- protein
- Length
- 971 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.85
- Source
- Human immunodeficiency virus type 1 group M subtype B (isolate BH10)
- Molecule
- Reverse transcriptase/ribonuclease H; p51 RT
- EC
- 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.1.13.2
- UniProt
- P03366
- Ligands
- 0IF, T27, MG, SO4
- Pockets
- 16 · best druggability 0.83
Structure
x-ray diffraction · resolution 1.85 · 2 distinct chains · 34% helix, 22% 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, 3.1.13.2) | protein | 556 | 33% helix, 23% strand | P03366 |
| B | p51 RT | protein | 415 | 36% helix, 19% strand | P03366 |
Ligands and binding sites
- 0IF · 2-amino-6-fluorobenzonitrile · ligand · chains A, B
- T27 · 4-{[4-({4-[(E)-2-cyanoethenyl]-2,6-dimethylphenyl}amino)pyrimidin-2-yl]amino}benzonitrile · ligand · chains A, B
- MG · Magnesium ion · metal · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 7 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 886 | 0.83 | 0.85 | 90 | 0IF, T27, EDO |
| 2 | 734 | 0.77 | 0.81 | 68 | DMS, SO4 |
| 3 | 585 | 0.71 | 0.79 | 48 | empty |
| 4 | 229 | 0.61 | 0.81 | 36 | DMS |
| 5 | 275 | 0.58 | 0.78 | 41 | DMS |
Interfaces
1 interface between chains.
- A–B · 2713 Ų buried · 26 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 8DXE · PDBe 8DXE · UniProt P03366
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