MolNFT v1 · #144043 · protein + DNA
Structure of HIV-1 reverse transcriptase bound to a 38-mer hairpin template-primer RNA-DNA aptamer
6BHJ · HIV-1 reverse transcriptase P66 subunit: “Structure of HIV-1 reverse transcriptase bound to a 38-mer hairpin template-primer RNA-DNA aptamer”. X-ray diffraction, 4 ligands (GLC, FRU, MG), 20 pockets (best druggability 0.82). MolNFT…
- PDB
- 6BHJ
- Type
- protein + DNA
- Length
- 2,003 residues
- Chains
- 6
- 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; 38-mer…
- UniProt
- A0A076Q3N8
- Ligands
- GLC, FRU, MG, SO4
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 5 distinct chains · 34% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HIV-1 reverse transcriptase P66 subunit | protein | 554 | 33% helix, 24% strand | A0A076Q3N8 |
| B | HIV-1 reverse transcriptase P51 subunit | protein | 416 | 36% helix, 19% strand | A0A076Q3N8 |
| C | HIV-1 reverse transcriptase P66 subunit | protein | 553 | 32% helix, 23% strand | A0A076Q3N8 |
| D | HIV-1 reverse transcriptase P51 subunit | protein | 410 | 36% helix, 20% strand | A0A076Q3N8 |
| E, F | 38-mer RNA-DNA aptamer | dna | 35 | — | — |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains B, D
- FRU · beta-D-fructofuranose · sugar · 2 copies · chains B, D
- MG · Magnesium ion · metal · 2 copies · chains A, C
- SO4 · Sulfate ion · ion · chains C
- GOL · Glycerol · additive · 6 copies · chains B, C, A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 890 | 0.82 | 0.84 | 83 | SO4, GOL |
| 2 | 319 | 0.81 | 0.91 | 47 | GOL |
| 3 | 505 | 0.81 | 0.87 | 52 | empty |
| 4 | 779 | 0.79 | 0.82 | 68 | empty |
| 5 | 1092 | 0.79 | 0.80 | 80 | MG |
Interfaces
8 interfaces between chains.
- A–B · 3019 Ų buried · 42 hydrogen bonds · protein-protein
- C–D · 2911 Ų buried · 34 hydrogen bonds · protein-protein
- A–E · 2092 Ų buried · 33 hydrogen bonds · protein-nucleic
- C–F · 2006 Ų buried · 32 hydrogen bonds · protein-nucleic
- B–C · 535 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6BHJ · Structure of HIV-1 Reverse Transcriptase Bound to a 38-mer Hairpin Template-Primer… · 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 A0A076Q3N8
- Elsewhere: RCSB PDB 6BHJ · PDBe 6BHJ · UniProt A0A076Q3N8
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