Research workbench
Structure of HIV-1 rt complexed with an RNA/DNA hybrid containing the polypurine-tract sequence
Analyse Structure of HIV-1 rt complexed with an RNA/DNA hybrid containing the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BSI
- 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
- 20 · best druggability 0.82
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 | 543 | 32% helix, 22% strand | Q74085 |
| B | Reverse transcriptase P51 subunit | protein | 406 | 38% helix, 19% strand | A0A076Q3N8 |
| D | DNA (5'- D(*GP*TP*TP*TP*TP*TP*CP*TP*TP*TP*TP*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, D
- GOL · Glycerol · additive · 2 copies · chains 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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 773 | 0.82 | 0.85 | 73 | empty |
| 2 | 1106 | 0.80 | 0.82 | 92 | empty |
| 3 | 580 | 0.75 | 0.82 | 47 | empty |
| 4 | 194 | 0.75 | 0.90 | 24 | EFZ |
| 5 | 346 | 0.68 | 0.81 | 40 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2658 Ų buried · 25 hydrogen bonds · protein-protein
- D–R · 990 Ų buried · 79 hydrogen bonds · nucleic-nucleic
- A–D · 968 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–R · 924 Ų buried · 12 hydrogen bonds · protein-nucleic
- B–D · 233 Ų buried · 4 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 6BSI · Structure of HIV-1 RT complexed with an RNA/DNA hybrid containing the polypurine-tract… · 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 6BSI · PDBe 6BSI · UniProt Q74085 · UniProt A0A076Q3N8
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