Research workbench
Crystal structure of HIV-1 reverse transcriptase in complex with 8-(2- (2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-YL)ETHOXY)PHENOXY) indolizine-2-carbonitrile (JLJ555), a non-nucleoside inhibitor
Analyse Crystal structure of HIV-1 reverse transcriptase in complex with 8-(2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MFB
- Type
- protein
- Length
- 957 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV-1 reverse transcriptase, P66 subunit; HIV-1 reverse transcriptase, P51 subunit
- EC
- 2.7.7.49
- UniProt
- P03366
- Ligands
- 29T
- Pockets
- 14 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HIV-1 reverse transcriptase, P66 subunit (EC 2.7.7.49) | protein | 544 | 30% helix, 22% strand | P03366 |
| B | HIV-1 reverse transcriptase, P51 subunit (EC 2.7.7.49) | protein | 413 | 37% helix, 19% strand | P03366 |
Ligands and binding sites
- 29T · 8-{2-[2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy]phenoxy}indolizine-2-carbonitrile · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1158 | 0.78 | 0.80 | 111 | empty |
| 2 | 746 | 0.75 | 0.80 | 76 | 29T |
| 3 | 560 | 0.70 | 0.79 | 52 | empty |
| 4 | 270 | 0.66 | 0.82 | 38 | empty |
| 5 | 404 | 0.66 | 0.79 | 49 | empty |
Interfaces
1 interface between chains.
- A–B · 2492 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 4MFB · Crystal Structure of HIV-1 Reverse Transcriptase 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 4MFB · PDBe 4MFB · UniProt P03366
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