Research workbench
5-se-T2-DNA and native RNA hybrid in complex with RNase H catalytic domain D132N mutant
Analyse 5-se-T2-DNA and native RNA hybrid in complex with RNase H catalytic domain… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5USA
- Type
- protein + DNA + RNA
- Length
- 144 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (5'-R(*UP*CP*GP*AP*CP*A)-3'); DNA (5'-D(*AP*(T5S)P*GP*TP*CP*G)-3'); Ribonuclease H
- EC
- 3.1.26.4
- UniProt
- Q9KEI9
- Ligands
- MG
- Pockets
- 1 · best druggability 0.26
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | RNA (5'-R(*UP*CP*GP*AP*CP*A)-3') | rna | 6 | — | — |
| C | DNA (5'-D(*AP*(T5S)P*GP*TP*CP*G)-3') | dna | 6 | — | — |
| A | Ribonuclease H (EC 3.1.26.4) | protein | 132 | 34% helix, 27% strand | Q9KEI9 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 56 | 0.26 | 0.74 | 12 | empty |
Interfaces
3 interfaces between chains.
- C–A · 440 Ų buried · 16 hydrogen bonds · protein-nucleic
- B–A · 280 Ų buried · 13 hydrogen bonds · protein-nucleic
- B–C · 272 Ų buried · 18 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 5USA · 5-Se-T2-DNA and native RNA hybrid in complex with RNase H catalytic domain D132N mutant · the same entry in another collection · chain B against B, TM-score 1.00
- Q9KEI9 · AlphaFold monomer V2.0 prediction for ribonuclease H (Q9KEI9) · a predicted model of the same protein · 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 Q9KEI9
- Elsewhere: RCSB PDB 5USA · PDBe 5USA · UniProt Q9KEI9
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