Research workbench
HIV-1 rt with pyridone non-nucleoside inhibitor
Analyse HIV-1 rt with pyridone non-nucleoside inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FFI
- Type
- protein
- Length
- 952 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reverse TRANSCRIPTASE/RIBONUCLEASE H; Rt P51
- EC
- 2.7.7.49, 2.7.7.7, 3.1.26.4
- UniProt
- P04585
- Ligands
- 3OB
- Pockets
- 15 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Reverse TRANSCRIPTASE/RIBONUCLEASE H (EC 2.7.7.49, 2.7.7.7, 3.1.26.4) | protein | 549 | 32% helix, 22% strand | P04585 |
| B | Rt P51 | protein | 403 | 38% helix, 18% strand | P04585 |
Ligands and binding sites
- 3OB · 3-chloro-5-({6-[2-(3,4-dihydroisoquinolin-2(1H)-yl)-2-oxoethyl]-3-(dimethylamino)-2-oxo-1,2-dihydropyridin-4-yl}oxy)benzonitrile · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 798 | 0.78 | 0.81 | 73 | 3OB |
| 2 | 433 | 0.71 | 0.82 | 38 | empty |
| 3 | 271 | 0.68 | 0.83 | 39 | empty |
| 4 | 254 | 0.61 | 0.80 | 29 | empty |
| 5 | 316 | 0.58 | 0.77 | 40 | empty |
Interfaces
1 interface between chains.
- A–B · 2837 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- 3FFI · HIV-1 RT with pyridone non-nucleoside inhibitor · 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 P04585
- Elsewhere: RCSB PDB 3FFI · PDBe 3FFI · UniProt P04585
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