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
- 1VRT
- Type
- protein
- Length
- 926 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
- NVP, MG
- Pockets
- 15 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HIV-1 reverse transcriptase (EC 2.7.7.49) | protein | 525 | 32% helix, 22% strand | P04585 |
| B | HIV-1 reverse transcriptase (EC 2.7.7.49) | protein | 401 | 36% helix, 20% strand | P04585 |
Ligands and binding sites
- NVP · 11-cyclopropyl-5,11-dihydro-4-methyl-6H-dipyrido[3,2-B:2',3'-e][1,4]diazepin-6-one · ligand · chains A
- MG · Magnesium ion · metal · 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 943 | 0.81 | 0.82 | 76 | NVP |
| 2 | 610 | 0.69 | 0.78 | 63 | empty |
| 3 | 471 | 0.63 | 0.76 | 37 | empty |
| 4 | 271 | 0.61 | 0.80 | 25 | empty |
| 5 | 151 | 0.60 | 0.84 | 34 | empty |
Interfaces
1 interface between chains.
- A–B · 2431 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 1VRT · 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 1VRT · PDBe 1VRT · UniProt P04585
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.