MolNFT v1 · #144405 · protein + DNA + RNA
Structure of HIV-1 rt complexed with RNA/DNA hybrid in the RNA hydrolysis mode
6BSH · Reverse transcriptase P66 subunit: “Structure of HIV-1 rt complexed with RNA/DNA hybrid in the RNA hydrolysis mode”. X-ray diffraction, 3 ligands (EFZ, TAM, CA), 19 pockets (best druggability 0.85). MolNFT v1 #144405 on GenesisL1…
- PDB
- 6BSH
- Type
- protein + DNA + RNA
- Length
- 996 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'…
- EC
- 2.7.7.7
- UniProt
- P03367, A0A076Q3N8
- Ligands
- EFZ, TAM, CA
- Pockets
- 19 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Reverse transcriptase P66 subunit (EC 2.7.7.7) | protein | 544 | 33% helix, 23% strand | P03367 |
| B | Reverse transcriptase P51 subunit | protein | 404 | 38% helix, 20% 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, B
- TAM · Tris(hydroxyethyl)aminomethane · ligand · chains D, R
- CA · Calcium ion · metal · 2 copies · chains A, R
- GOL · Glycerol · additive · 6 copies · chains A, B, R, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 985 | 0.85 | 0.86 | 104 | empty |
| 2 | 825 | 0.80 | 0.83 | 59 | GOL |
| 3 | 148 | 0.76 | 0.93 | 21 | EFZ |
| 4 | 266 | 0.68 | 0.83 | 37 | empty |
| 5 | 119 | 0.60 | 0.86 | 23 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2585 Ų buried · 21 hydrogen bonds · protein-protein
- A–R · 1261 Ų buried · 33 hydrogen bonds · protein-nucleic
- D–R · 1109 Ų buried · 116 hydrogen bonds · nucleic-nucleic
- A–D · 1072 Ų buried · 24 hydrogen bonds · protein-nucleic
- B–D · 240 Ų buried · 4 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 6BSH · Structure of HIV-1 RT complexed with RNA/DNA hybrid in the RNA hydrolysis mode · the same entry in another collection · chain B against B, 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 P03367
- Every structure of UniProt A0A076Q3N8
- Elsewhere: RCSB PDB 6BSH · PDBe 6BSH · UniProt P03367 · UniProt A0A076Q3N8
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