Research workbench
Human RNase H catalytic domain mutant D210N in complex with 20-mer RNA/DNA hybrid
Analyse Human RNase H catalytic domain mutant D210N in complex with 20-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
- 2QKB
- Type
- protein + DNA + RNA
- Length
- 341 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-R(*GP*GP*AP*GP*UP*GP*CP*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP *CP*C)-3')…
- EC
- 3.1.26.4
- UniProt
- O60930
- Ligands
- SO4
- Pockets
- 1 · best druggability 0.63
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | 5'-R(*GP*GP*AP*GP*UP*GP*CP*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP *CP*C)-3') | rna | 19 | — | — |
| D | 5'-D(*DGP*DGP*DAP*DAP*DTP*DCP*DAP*DGP*DGP*DTP*DGP*DTP*DCP*D GP*DCP*DAP*DCP*DTP*DCP*DT)-3' | dna | 20 | — | — |
| A | Ribonuclease H1 (EC 3.1.26.4) | protein | 152 | 38% helix, 25% strand | O60930 |
| B | Ribonuclease H1 (EC 3.1.26.4) | protein | 150 | 37% helix, 25% strand | O60930 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 753 | 0.63 | 0.73 | 48 | empty |
Interfaces
5 interfaces between chains.
- C–D · 906 Ų buried · 93 hydrogen bonds · nucleic-nucleic
- D–A · 566 Ų buried · 16 hydrogen bonds · protein-nucleic
- D–B · 527 Ų buried · 16 hydrogen bonds · protein-nucleic
- C–A · 505 Ų buried · 28 hydrogen bonds · protein-nucleic
- C–B · 462 Ų buried · 20 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 2QKB · Human RNase H catalytic domain mutant D210N in complex with 20-mer RNA/DNA hybrid · the same entry in another collection · chain C against C, TM-score 1.00
- O60930 · AlphaFold monomer V2.0 prediction for ribonuclease H1 (O60930) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 2QKB · PDBe 2QKB · UniProt O60930
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