MolNFT v1 · #139681 · protein + DNA
HIV-1 reverse transcriptase Q151M:DNA:ENTECAVIR-triphosphate ternary complex
5XN1 · Pol protein: “HIV-1 reverse transcriptase Q151M:DNA:ENTECAVIR-triphosphate ternary complex”. X-ray diffraction, 4 ligands (ET9, GLC, FRU), 20 pockets (best druggability 0.82). MolNFT v1 #139681 on GenesisL1: 3D structure, binding…
- PDB
- 5XN1
- Type
- protein + DNA
- Length
- 1,989 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pol protein; 38-mer DNA aptamer
- UniProt
- D3XFN7
- Ligands
- ET9, GLC, FRU, MG
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Pol protein | protein | 551 | 33% helix, 24% strand | D3XFN7 |
| B, D | Pol protein | protein | 407 | 35% helix, 19% strand | D3XFN7 |
| E | 38-mer DNA aptamer | dna | 35 | — | — |
| F | 38-mer DNA aptamer | dna | 38 | — | — |
Ligands and binding sites
- ET9 · [[(1R,3S,5S)-3-(2-azanyl-6-oxidanylidene-3H-purin-9-yl)-2-methylidene-5-oxidanyl-cyclopentyl]methoxy-oxidanyl-phosphory l] phosphono hydrogen phosphate · ligand · 2 copies · chains A, E, C, F
- GLC · alpha-D-glucopyranose · sugar · chains B
- FRU · beta-D-fructofuranose · sugar · chains B, E
- MG · Magnesium ion · metal · 2 copies · chains A, C
- GOL · Glycerol · additive · 5 copies · chains A, B, C, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 304 | 0.82 | 0.93 | 40 | GOL |
| 2 | 326 | 0.81 | 0.92 | 41 | GOL |
| 3 | 365 | 0.80 | 0.89 | 57 | GOL |
| 4 | 997 | 0.76 | 0.78 | 100 | empty |
| 5 | 493 | 0.75 | 0.83 | 53 | empty |
Interfaces
7 interfaces between chains.
- C–D · 2935 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 2925 Ų buried · 33 hydrogen bonds · protein-protein
- C–F · 1979 Ų buried · 23 hydrogen bonds · protein-nucleic
- A–E · 1901 Ų buried · 23 hydrogen bonds · protein-nucleic
- A–C · 822 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 5XN1 · HIV-1 reverse transcriptase Q151M:DNA:entecavir-triphosphate ternary complex · 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 D3XFN7
- Elsewhere: RCSB PDB 5XN1 · PDBe 5XN1 · UniProt D3XFN7
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.