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Crystal structure of K103N/Y181C mutant HIV-1 reverse transcriptase (RT) in complex with TMC278 (Rilpivirine), a non-nucleoside RT inhibitor
Analyse Crystal structure of K103N/Y181C mutant HIV-1 reverse transcriptase (RT) in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BGR
- Type
- protein
- Length
- 966 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.1
- Source
- Human immunodeficiency virus 1
- Molecule
- Reverse transcriptase/ribonuclease H; p51 RT
- EC
- 2.7.7.49, 2.7.7.7, 3.1.26.4
- UniProt
- P03366
- Ligands
- T27
- Pockets
- 16 · best druggability 0.82
Structure
x-ray diffraction · resolution 2.1 · 2 distinct chains · 33% helix, 22% 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 | 554 | 32% helix, 23% strand | P03366 |
| B | p51 RT | protein | 412 | 35% helix, 20% strand | P03366 |
Ligands and binding sites
- T27 · 4-{[4-({4-[(E)-2-cyanoethenyl]-2,6-dimethylphenyl}amino)pyrimidin-2-yl]amino}benzonitrile · ligand · chains A, B
- EDO · 1,2-ethanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 970 | 0.82 | 0.83 | 88 | T27 |
| 2 | 579 | 0.78 | 0.84 | 46 | empty |
| 3 | 77 | 0.73 | 0.97 | 19 | empty |
| 4 | 655 | 0.71 | 0.78 | 47 | empty |
| 5 | 330 | 0.60 | 0.78 | 44 | empty |
Interfaces
1 interface between chains.
- A–B · 2635 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 3BGR · Crystal structure of K103N/Y181C mutant 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 3BGR · PDBe 3BGR · UniProt P03366
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