Research workbench
Crystal structure of LC11-RNase H1 in complex with RNA/DNA hybrid
Analyse Crystal structure of LC11-RNase H1 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
- 4H8K
- Type
- protein + DNA + RNA
- Length
- 304 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease H; RNA (5'-R(*CP*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*CP*C)-3'); DNA…
- EC
- 3.1.26.4
- UniProt
- E0X767
- Pockets
- 3 · best druggability 0.49
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ribonuclease H (EC 3.1.26.4) | protein | 138 | 45% helix, 30% strand | E0X767 |
| C | RNA (5'-R(*CP*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*CP*C)-3') | rna | 14 | — | — |
| D | DNA (5'-D(*GP*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*CP*G)-3') | dna | 14 | — | — |
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 103 | 0.49 | 0.81 | 18 | empty |
| 2 | 82 | 0.43 | 0.79 | 21 | empty |
| 3 | 53 | 0.22 | 0.72 | 5 | empty |
Interfaces
5 interfaces between chains.
- C–D · 686 Ų buried · 68 hydrogen bonds · nucleic-nucleic
- B–C · 512 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–C · 496 Ų buried · 11 hydrogen bonds · protein-nucleic
- B–D · 446 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–D · 445 Ų buried · 14 hydrogen bonds · protein-nucleic
Compared structures
- 4H8K · Crystal structure of LC11-RNase H1 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 E0X767
- Elsewhere: RCSB PDB 4H8K · PDBe 4H8K · UniProt E0X767
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