MolNFT v1 · #144404 · protein + DNA + RNA
Structure of HIV-1 rt complexed with RNA/DNA hybrid in an RNA hydrolysis-off mode
6BSG · Reverse transcriptase P66 subunit: “Structure of HIV-1 rt complexed with RNA/DNA hybrid in an RNA hydrolysis-off mode”. X-ray diffraction, 2 ligands (EFZ, CA), 19 pockets (best druggability 0.81). MolNFT v1 #144404 on GenesisL1: 3D…
- PDB
- 6BSG
- Type
- protein + DNA + RNA
- Length
- 997 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reverse transcriptase P66 subunit; Reverse transcriptase P51 subunit; DNA (5'…
- UniProt
- Q74085, A0A076Q3N8
- Ligands
- EFZ, CA
- Pockets
- 19 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Reverse transcriptase P66 subunit | protein | 545 | 32% helix, 22% strand | Q74085 |
| B | Reverse transcriptase P51 subunit | protein | 404 | 39% helix, 21% strand | A0A076Q3N8 |
| D | DNA (5'- D(*GP*TP*AP*TP*GP*CP*CP*AP*CP*TP*AP*GP*TP*TP*AP*TP*TP*GP*TP*GP*GP*CP* C)-3') | dna | 23 | — | — |
| R | RNA (25-mer) | rna | 25 | — | — |
Ligands and binding sites
- EFZ · (-)-6-chloro-4-cyclopropylethynyl-4-trifluoromethyl-1, 4-dihydro-2H-3,1-benzoxazin-2-one · ligand · chains A
- CA · Calcium ion · metal · 2 copies · chains A, R
- GOL · Glycerol · additive · 4 copies · chains A, B, R, D
- PEG · Di(hydroxyethyl)ether · additive · chains D, R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 856 | 0.81 | 0.83 | 77 | empty |
| 2 | 761 | 0.80 | 0.83 | 51 | empty |
| 3 | 435 | 0.75 | 0.85 | 44 | empty |
| 4 | 666 | 0.75 | 0.80 | 62 | EFZ |
| 5 | 289 | 0.68 | 0.83 | 30 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2568 Ų buried · 31 hydrogen bonds · protein-protein
- A–R · 1133 Ų buried · 25 hydrogen bonds · protein-nucleic
- D–R · 1102 Ų buried · 113 hydrogen bonds · nucleic-nucleic
- A–D · 1038 Ų buried · 17 hydrogen bonds · protein-nucleic
- B–D · 240 Ų buried · 5 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 6BSG · Structure of HIV-1 RT complexed with RNA/DNA hybrid in an RNA hydrolysis-off mode · 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 Q74085
- Every structure of UniProt A0A076Q3N8
- Elsewhere: RCSB PDB 6BSG · PDBe 6BSG · UniProt Q74085 · UniProt A0A076Q3N8
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