Research workbench
HIV-1 rt with non-nucleoside inhibitor annulated pyrazole 1
Analyse HIV-1 rt with non-nucleoside inhibitor annulated pyrazole 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DYA
- Type
- protein
- Length
- 953 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reverse TRANSCRIPTASE/RIBONUCLEASE H; P51 rt
- EC
- 2.7.7.49, 2.7.7.7, 3.1.26.4
- UniProt
- P04585
- Ligands
- PZL
- Pockets
- 13 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 35% 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, 3.1.26.4) | protein | 551 | 33% helix, 23% strand | P04585 |
| B | P51 rt (EC 2.7.7.49, 2.7.7.7, 3.1.26.4) | protein | 402 | 39% helix, 18% strand | P04585 |
Ligands and binding sites
- PZL · 3-[6-bromo-2-fluoro-3-(1H-pyrazolo[3,4-c]pyridazin-3-ylmethyl)phenoxy]-5-chlorobenzonitrile · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1104 | 0.79 | 0.80 | 123 | PZL |
| 2 | 693 | 0.75 | 0.80 | 65 | empty |
| 3 | 234 | 0.65 | 0.83 | 40 | empty |
| 4 | 153 | 0.47 | 0.76 | 17 | empty |
| 5 | 135 | 0.45 | 0.77 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 2866 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 3DYA · HIV-1 RT with non-nucleoside inhibitor annulated Pyrazole 1 · 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 3DYA · PDBe 3DYA · UniProt P04585
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