MolNFT v1 · #49312 · protein + DNA + RNA
Human RNase H catalytic domain mutant D210N in complex with 18-mer RNA/DNA hybrid
2QK9 · 5'-R(*AP*GP*UP*GP*CP*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*CP*C)…: “Human RNase H catalytic domain mutant D210N in complex with 18-mer RNA/DNA hybrid”. X-ray diffraction, 3 ligands (16D, NA, SO4), 2 pockets (best druggability 0.55).…
- PDB
- 2QK9
- Type
- protein + DNA + RNA
- Length
- 189 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-R(*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
- 16D, NA, SO4
- Pockets
- 2 · best druggability 0.55
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | 5'-R(*AP*GP*UP*GP*CP*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*CP*C) -3' | rna | 18 | — | — |
| C | 5'-D(*GP*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*CP*GP*CP*AP*CP*T) -3' | dna | 18 | — | — |
| A | Ribonuclease H1 (EC 3.1.26.4) | protein | 153 | 37% helix, 23% strand | O60930 |
Ligands and binding sites
- 16D · Hexane-1,6-diamine · ligand · chains B, C
- NA · Sodium ion · metal · chains B, A
- SO4 · Sulfate ion · ion · 7 copies · chains B, C, A
- GOL · Glycerol · additive · 2 copies · chains A
- FLC · Citrate anion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 419 | 0.55 | 0.74 | 19 | SO4 |
| 2 | 168 | 0.46 | 0.76 | 19 | SO4 |
Interfaces
3 interfaces between chains.
- B–C · 864 Ų buried · 84 hydrogen bonds · nucleic-nucleic
- B–A · 591 Ų buried · 26 hydrogen bonds · protein-nucleic
- C–A · 586 Ų buried · 18 hydrogen bonds · protein-nucleic
Compared structures
- 2QK9 · Human RNase H catalytic domain mutant D210N in complex with 18-mer RNA/DNA hybrid · the same entry in another collection · chain B against B, 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 2QK9 · PDBe 2QK9 · UniProt O60930
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