Research workbench
High resolution structures of HIV-1 rt from four rt- inhibitor complexes
Analyse High resolution structures of HIV-1 rt from four rt- inhibitor complexes in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1VRU
- Type
- protein
- Length
- 936 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV-1 reverse transcriptase
- EC
- 2.7.7.49
- UniProt
- P04585
- Ligands
- AAP
- Pockets
- 15 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HIV-1 reverse transcriptase (EC 2.7.7.49) | protein | 526 | 32% helix, 22% strand | P04585 |
| B | HIV-1 reverse transcriptase (EC 2.7.7.49) | protein | 410 | 37% helix, 19% strand | P04585 |
Ligands and binding sites
- AAP · Alpha-(2,6-dichlorophenyl)-alpha-(2-acetyl-5-methylanilino)acetamide · ligand · 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 | 753 | 0.78 | 0.82 | 69 | AAP |
| 2 | 714 | 0.71 | 0.78 | 62 | empty |
| 3 | 523 | 0.68 | 0.78 | 41 | empty |
| 4 | 541 | 0.66 | 0.77 | 60 | empty |
| 5 | 178 | 0.61 | 0.83 | 34 | empty |
Interfaces
1 interface between chains.
- A–B · 2442 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 1VRU · High resolution structures of HIV-1 rt from four rt-inhibitor complexes · 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 1VRU · PDBe 1VRU · UniProt P04585
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