Research workbench
HIV-1 Reverse Transcriptase in complex with a phosphonate analog of nevirapine
Analyse HIV-1 Reverse Transcriptase in complex with a phosphonate analog of nevirapine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4I7F
- Type
- protein
- Length
- 957 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.5
- Source
- HIV-1 M:B_HXB2R
- Molecule
- Reverse transcriptase
- EC
- 2.7.7.49
- UniProt
- P04585
- Ligands
- NVE, MG, SO4, CL
- Pockets
- 15 · best druggability 0.80
Structure
x-ray diffraction · resolution 2.5 · 2 distinct chains · 34% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Reverse transcriptase (EC 2.7.7.49) | protein | 552 | 32% helix, 24% strand | P04585 |
| B | Reverse transcriptase (EC 2.7.7.49) | protein | 405 | 37% helix, 20% strand | P04585 |
Ligands and binding sites
- NVE · diethyl ({4-[2-(11-ethyl-5-methyl-6-oxo-6,11-dihydro-5H-dipyrido[3,2-b:2',3'-e][1,4]diazepin-8-yl)ethyl]phenoxy}methyl)phosphonate · ligand · chains A, B
- MG · Magnesium ion · metal · chains A
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- CL · Chloride ion · ion · 2 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 990 | 0.80 | 0.82 | 105 | NVE |
| 2 | 502 | 0.71 | 0.80 | 42 | empty |
| 3 | 274 | 0.67 | 0.83 | 38 | empty |
| 4 | 347 | 0.57 | 0.75 | 45 | CL |
| 5 | 199 | 0.57 | 0.80 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 2726 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 4I7F · HIV-1 reverse transcriptase in complex with a phosphonate analog of nevirapine · 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 4I7F · PDBe 4I7F · UniProt P04585
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