Research workbench
Crystal structure of Y188C mutant HIV-1 reverse transcriptase in complex with uc-781
Analyse Crystal structure of Y188C mutant HIV-1 reverse transcriptase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1JLG
- Type
- protein
- Length
- 936 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.6
- Source
- HIV-1 M:B_HXB2R
- Molecule
- HIV-1 RT A-chain; HIV-1 RT B-chain
- EC
- 2.7.7.49
- UniProt
- P04585
- Ligands
- UC1
- Pockets
- 17 · best druggability 0.79
Structure
x-ray diffraction · resolution 2.6 · 2 distinct chains · 33% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HIV-1 RT A-chain (EC 2.7.7.49) | protein | 531 | 33% helix, 24% strand | P04585 |
| B | HIV-1 RT B-chain (EC 2.7.7.49) | protein | 405 | 34% helix, 20% strand | P04585 |
Ligands and binding sites
- UC1 · 2-methyl-furan-3-carbothioic acid [4-chloro-3-(3-methyl-but-2-enyloxy)-phenyl]-amide · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 943 | 0.79 | 0.81 | 80 | UC1 |
| 2 | 439 | 0.75 | 0.84 | 45 | empty |
| 3 | 445 | 0.65 | 0.78 | 38 | empty |
| 4 | 108 | 0.63 | 0.88 | 20 | empty |
| 5 | 285 | 0.57 | 0.77 | 35 | empty |
Interfaces
1 interface between chains.
- A–B · 2563 Ų buried · 29 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 1JLG · Crystal structure of Y188C mutant HIV-1 reverse transcriptase in complex with uc-781 · 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 1JLG · PDBe 1JLG · UniProt P04585
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