Research workbench
Hybrid-binding domain of human RNase H1 in complex with 12- mer RNA/DNA
Analyse Hybrid-binding domain of human RNase H1 in complex with 12- mer RNA/DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BSU
- Type
- protein + DNA + RNA
- Length
- 338 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease H1; RNA (5'-R(*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*C)- 3'); DNA…
- EC
- 3.1.26.4
- UniProt
- O60930
- Ligands
- MG
- Pockets
- 6 · best druggability 0.61
Structure
x-ray diffraction · 7 distinct chains · 34% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ribonuclease H1 (EC 3.1.26.4) | protein | 48 | 35% helix, 29% strand | O60930 |
| C | Ribonuclease H1 (EC 3.1.26.4) | protein | 48 | 35% helix, 29% strand | O60930 |
| D, I | RNA (5'-R(*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*C)- 3') | rna | 12 | — | — |
| E, J | DNA (5'-D(*DGP*DAP*DAP*DTP*DCP*DAP*DGP*DGP*(5IU) P*DGP*DTP*DC)-3') | dna | 12 | — | — |
| F | Ribonuclease H1 (EC 3.1.26.4) | protein | 49 | 35% helix, 29% strand | O60930 |
| G | Ribonuclease H1 (EC 3.1.26.4) | protein | 50 | 32% helix, 28% strand | O60930 |
| H | Ribonuclease H1 (EC 3.1.26.4) | protein | 47 | 34% helix, 30% strand | O60930 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 460 | 0.61 | 0.77 | 30 | empty |
| 2 | 486 | 0.61 | 0.76 | 36 | empty |
| 3 | 170 | 0.60 | 0.83 | 29 | empty |
| 4 | 140 | 0.54 | 0.82 | 24 | empty |
| 5 | 112 | 0.53 | 0.83 | 22 | empty |
Interfaces
23 interfaces between chains.
- D–E · 550 Ų buried · 57 hydrogen bonds · nucleic-nucleic
- I–J · 548 Ų buried · 49 hydrogen bonds · nucleic-nucleic
- A–E · 291 Ų buried · 4 hydrogen bonds · protein-nucleic
- H–J · 288 Ų buried · 4 hydrogen bonds · protein-nucleic
- F–J · 288 Ų buried · 4 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
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 O60930
- Elsewhere: RCSB PDB 3BSU · PDBe 3BSU · UniProt O60930
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