Research workbench
Xmrv reverse transcriptase in complex with RNA/DNA hybrid
Analyse Xmrv reverse transcriptase in complex with 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
- 4HKQ
- Type
- protein + DNA + RNA
- Length
- 471 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reverse TRANSCRIPTASE/RIBONUCLEASE H P80; RNA (5'…
- EC
- 2.7.7.49, 2.7.7.7, 3.1.26.4
- UniProt
- A1Z651
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Reverse TRANSCRIPTASE/RIBONUCLEASE H P80 (EC 2.7.7.49, 2.7.7.7, 3.1.26.4) | protein | 441 | 36% helix, 23% strand | A1Z651 |
| E | RNA (5'- R(*AP*AP*CP*AP*GP*AP*GP*UP*GP*CP*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*CP* CP*AP*U)-3') | rna | 16 | — | — |
| F | DNA (5'- D(*TP*GP*GP*AP*AP*TP*CP*A*GP*GP*TP*GP*TP*CP*GP*CP*AP*CP*TP*CP*TP*G)- 3') | dna | 14 | — | — |
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 113 | 0.77 | 0.97 | 30 | empty |
| 2 | 273 | 0.62 | 0.80 | 31 | empty |
| 3 | 96 | 0.59 | 0.88 | 18 | empty |
| 4 | 284 | 0.48 | 0.73 | 27 | empty |
| 5 | 55 | 0.35 | 0.78 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–E · 1019 Ų buried · 11 hydrogen bonds · protein-nucleic
- E–F · 704 Ų buried · 87 hydrogen bonds · nucleic-nucleic
- A–F · 658 Ų buried · 9 hydrogen bonds · protein-nucleic
Compared structures
- 4HKQ · XMRV reverse transcriptase in complex with 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 A1Z651
- Elsewhere: RCSB PDB 4HKQ · PDBe 4HKQ · UniProt A1Z651
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