Research workbench
Crystal structure of HIV-1 reverse transcriptase (rt) in complex with R221239
Analyse Crystal structure of HIV-1 reverse transcriptase (rt) in complex with R221239 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2BE2
- Type
- protein
- Length
- 978 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reverse transcriptase P66 subunit; Reverse transcriptase P51 subunit
- EC
- 2.7.7.49
- UniProt
- P03366
- Ligands
- R22, GLC, FRU, MN
- Pockets
- 15 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Reverse transcriptase P66 subunit (EC 2.7.7.49) | protein | 552 | 32% helix, 23% strand | P03366 |
| B | Reverse transcriptase P51 subunit (EC 2.7.7.49) | protein | 426 | 34% helix, 19% strand | P03366 |
Ligands and binding sites
- R22 · 4-(3,5-dimethylphenoxy)-5-(furan-2-ylmethylsulfanylmethyl)-3-iodo-6-methylpyridin-2(1H)-one · ligand · chains A
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A, B
- FRU · beta-D-fructofuranose · sugar · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · chains A
- GOL · Glycerol · additive · 2 copies · 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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 984 | 0.77 | 0.79 | 87 | empty |
| 2 | 799 | 0.75 | 0.79 | 65 | empty |
| 3 | 285 | 0.74 | 0.87 | 47 | R22 |
| 4 | 633 | 0.74 | 0.80 | 48 | empty |
| 5 | 555 | 0.68 | 0.78 | 52 | empty |
Interfaces
1 interface between chains.
- A–B · 2637 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 2BE2 · Crystal structure of HIV-1 reverse transcriptase (RT) in complex with R221239 · 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 P03366
- Elsewhere: RCSB PDB 2BE2 · PDBe 2BE2 · UniProt P03366
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.