MolNFT v1 · #168729 · protein + DNA
Structure of HIV-1 reverse transcriptase (rt) in complex with dsdna and (-)-ftc
6WPH · Reverse TRANSCRIPTASE/RIBONUCLEASE H: “Structure of HIV-1 reverse transcriptase (rt) in complex with dsdna and (-)-ftc”. X-ray diffraction, 4 ligands (43X, DG, MG), 14 pockets (best druggability 0.86). MolNFT v1 #168729 on…
- PDB
- 6WPH
- Type
- protein + DNA
- Length
- 979 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reverse TRANSCRIPTASE/RIBONUCLEASE H; P51 rt; DNA primer 21-mer; DNA template 27-mer
- EC
- 2.7.7.49, 2.7.7.7, 3.1.26.13, 2.7.7.-, 3.1.-.-
- UniProt
- P04585
- Ligands
- 43X, DG, MG, SO4
- Pockets
- 14 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Reverse TRANSCRIPTASE/RIBONUCLEASE H (EC 2.7.7.49, 2.7.7.7, 3.1.26.13) | protein | 548 | 34% helix, 23% strand | P04585 |
| B | P51 rt (EC 2.7.7.-, 3.1.-.-) | protein | 391 | 37% helix, 21% strand | P04585 |
| P | DNA primer 21-mer | dna | 18 | — | — |
| T | DNA template 27-mer | dna | 22 | — | — |
Ligands and binding sites
- 43X · [(2R,5S)-5-(4-amino-5-fluoro-2-oxopyrimidin-1(2H)-yl)-1,3-oxathiolan-2-yl]methyl dihydrogen phosphate · ligand · chains A, P, T
- DG · 2'-deoxyguanosine-5'-monophosphate · ligand · chains T
- MG · Magnesium ion · metal · 2 copies · chains A, T, B
- SO4 · Sulfate ion · ion · 2 copies · chains P, T
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 833 | 0.86 | 0.88 | 84 | empty |
| 2 | 972 | 0.85 | 0.86 | 93 | empty |
| 3 | 414 | 0.70 | 0.81 | 40 | empty |
| 4 | 485 | 0.68 | 0.79 | 50 | empty |
| 5 | 287 | 0.62 | 0.80 | 31 | 43X |
Interfaces
6 interfaces between chains.
- A–B · 3028 Ų buried · 33 hydrogen bonds · protein-protein
- A–T · 1265 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–P · 996 Ų buried · 10 hydrogen bonds · protein-nucleic
- P–T · 831 Ų buried · 73 hydrogen bonds · nucleic-nucleic
- B–P · 108 Ų buried · 1 hydrogen bond · protein-nucleic
Modifications
Observed in the structure: 1 covalent, 1 modified (covalent ligand, nucleotide modification).
Compared structures
- 6WPH · Structure of HIV-1 Reverse Transcriptase (RT) in complex with dsDNA and (-)-FTC · 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 P04585
- Elsewhere: RCSB PDB 6WPH · PDBe 6WPH · UniProt P04585
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