Research workbench
HIV-1 reverse transcriptase in complex with inhibitor GSK500
Analyse HIV-1 reverse transcriptase in complex with inhibitor GSK500 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YNH
- Type
- protein
- Length
- 966 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, 3.1.26.13, 3.1.13.2
- UniProt
- P04585
- Ligands
- EUR
- Pockets
- 18 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 34% 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, 3.1.13.2) | protein | 560 | 32% helix, 23% strand | P04585 |
| B | P51 rt | protein | 406 | 36% helix, 19% strand | P04585 |
Ligands and binding sites
- EUR · 4-chloranyl-N-[[4-chloranyl-3-(3-chloranyl-5-cyano-phenoxy)-2-fluoranyl-phenyl]methyl]-2-(hydroxymethyl)-1H-imidazole-5-carboxamide · ligand · chains A
- TAR · D(-)-tartaric acid · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 704 | 0.77 | 0.82 | 73 | EUR |
| 2 | 287 | 0.68 | 0.83 | 41 | empty |
| 3 | 348 | 0.65 | 0.80 | 32 | empty |
| 4 | 326 | 0.62 | 0.78 | 46 | empty |
| 5 | 221 | 0.61 | 0.81 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 2941 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 2YNH · HIV-1 Reverse Transcriptase in complex with inhibitor GSK500 · 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 2YNH · PDBe 2YNH · UniProt P04585
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