Research workbench
Crystal structure of HIV-1 reverse transcriptase (rt) in complex with 4-[(4-{4-[(E)-2-cyanoethenyl]-2,6-DIMETHYLPHENOXY}THIENO[3,2- D]PYRIMIDIN-2-YL)AMINO]-2-fluorobenzonitrile (24B), a non-nucleoside rt inhibitor
Analyse Crystal structure of HIV-1 reverse transcriptase (rt) 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
- 6UL5
- Type
- protein
- Length
- 972 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reverse transcriptase P66; Reverse transcriptase P51
- EC
- 2.7.7.49
- UniProt
- P03366
- Ligands
- QAG, MG, SO4
- Pockets
- 15 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Reverse transcriptase P66 (EC 2.7.7.49) | protein | 556 | 31% helix, 24% strand | P03366 |
| B | Reverse transcriptase P51 | protein | 416 | 35% helix, 19% strand | P03366 |
Ligands and binding sites
- QAG · 4-[(4-{4-[(E)-2-cyanoethenyl]-2,6-dimethylphenoxy}thieno[3,2-d]pyrimidin-2-yl)amino]-2-fluorobenzonitrile · ligand · chains A, B
- MG · Magnesium ion · metal · chains A
- SO4 · Sulfate ion · ion · 7 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 981 | 0.82 | 0.83 | 107 | QAG, EDO |
| 2 | 545 | 0.75 | 0.83 | 49 | SO4 |
| 3 | 681 | 0.73 | 0.79 | 48 | empty |
| 4 | 277 | 0.69 | 0.84 | 37 | SO4 |
| 5 | 299 | 0.58 | 0.77 | 40 | EDO |
Interfaces
1 interface between chains.
- A–B · 2744 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 6UL5 · Crystal structure of HIV-1 reverse transcriptase (RT) in complex with… · 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 6UL5 · PDBe 6UL5 · UniProt P03366
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