MolNFT v1 · #144407 · protein + DNA + RNA
Structure of HIV-1 rt complexed with an RNA/DNA hybrid sequence non- preferred for RNA hydrolysis
6BSJ · Reverse transcriptase P66 subunit: “Structure of HIV-1 rt complexed with an RNA/DNA hybrid sequence non- preferred for RNA hydrolysis”. X-ray diffraction, 3 ligands (EFZ, TAM, CA), 20 pockets (best druggability 0.83). MolNFT v1…
- PDB
- 6BSJ
- Type
- protein + DNA + RNA
- Length
- 991 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, TAM, CA
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Reverse transcriptase P66 subunit | protein | 543 | 33% helix, 22% strand | Q74085 |
| B | Reverse transcriptase P51 subunit | protein | 400 | 39% helix, 19% strand | A0A076Q3N8 |
| D | DNA (5'- D(*GP*TP*AP*TP*GP*CP*CP*TP*AP*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
- TAM · Tris(hydroxyethyl)aminomethane · ligand · chains D, R
- CA · Calcium ion · metal · chains A, R
- GOL · Glycerol · additive · 4 copies · chains A, D, R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1078 | 0.83 | 0.84 | 92 | empty |
| 2 | 462 | 0.80 | 0.88 | 59 | empty |
| 3 | 699 | 0.76 | 0.81 | 70 | EFZ |
| 4 | 275 | 0.75 | 0.88 | 33 | empty |
| 5 | 304 | 0.68 | 0.82 | 36 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2553 Ų buried · 16 hydrogen bonds · protein-protein
- D–R · 1057 Ų buried · 111 hydrogen bonds · nucleic-nucleic
- A–R · 1057 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–D · 767 Ų buried · 10 hydrogen bonds · protein-nucleic
- B–D · 205 Ų buried · 5 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 6BSJ · Structure of HIV-1 RT complexed with an RNA/DNA hybrid sequence non-preferred for RNA… · 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 6BSJ · PDBe 6BSJ · UniProt Q74085 · UniProt A0A076Q3N8
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