Research workbench
Rtx (reverse transcription xenopolymerase) in complex with an RNA/DNA hybrid
Analyse Rtx (reverse transcription xenopolymerase) in complex with an RNA/DNA hybrid in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WYB
- Type
- protein + DNA + RNA
- Length
- 762 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase; RNA strand; DNA strand
- EC
- 2.7.7.7
- UniProt
- D0VWU9
- Ligands
- TCE, SO4
- Pockets
- 10 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase (EC 2.7.7.7) | protein | 739 | 42% helix, 23% strand | D0VWU9 |
| B | RNA strand | rna | 11 | — | — |
| C | DNA strand | dna | 12 | — | — |
Ligands and binding sites
- TCE · 3,3',3''-phosphanetriyltripropanoic acid · ligand · chains A
- SO4 · Sulfate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 815 | 0.83 | 0.86 | 76 | empty |
| 2 | 447 | 0.60 | 0.75 | 45 | empty |
| 3 | 251 | 0.56 | 0.77 | 22 | EDO |
| 4 | 250 | 0.54 | 0.77 | 34 | SO4 |
| 5 | 156 | 0.49 | 0.77 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–C · 696 Ų buried · 17 hydrogen bonds · protein-nucleic
- A–B · 642 Ų buried · 8 hydrogen bonds · protein-nucleic
- B–C · 535 Ų buried · 42 hydrogen bonds · nucleic-nucleic
Compared structures
- 6WYB · RTX (Reverse Transcription Xenopolymerase) in complex with an RNA/DNA hybrid · 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 D0VWU9
- Elsewhere: RCSB PDB 6WYB · PDBe 6WYB · UniProt D0VWU9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.