Research workbench
Crystal structure of HIV-1 reverse transcriptase in complex with 5-(2- (2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-YL)ETHOXY)PHENOXY)-2- naphthonitrile (JLJ600)
Analyse Crystal structure of HIV-1 reverse transcriptase in complex with 5-(2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WE1
- Type
- protein
- Length
- 944 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gag-pol polyprotein
- EC
- 3.4.23.16, 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.1.13.2
- UniProt
- P03366
- Ligands
- 3LQ, MG, SO4
- Pockets
- 16 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gag-pol polyprotein (EC 3.4.23.16, 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.1.13.2) | protein | 542 | 31% helix, 22% strand | P03366 |
| B | Gag-pol polyprotein (EC 3.4.23.16, 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.1.13.2) | protein | 402 | 37% helix, 19% strand | P03366 |
Ligands and binding sites
- 3LQ · 5-{2-[2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy]phenoxy}naphthalene-2-carbonitrile · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
- SO4 · Sulfate ion · ion · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 716 | 0.76 | 0.81 | 84 | empty |
| 2 | 750 | 0.76 | 0.80 | 75 | 3LQ |
| 3 | 353 | 0.62 | 0.78 | 44 | empty |
| 4 | 268 | 0.59 | 0.79 | 37 | empty |
| 5 | 205 | 0.59 | 0.80 | 38 | empty |
Interfaces
1 interface between chains.
- A–B · 2602 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 4WE1 · 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 4WE1 · PDBe 4WE1 · UniProt P03366
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