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Crystal structure of RNase Z
Analyse Crystal structure of RNase Z in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Y44
- Type
- protein
- Length
- 566 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.1
- Source
- Bacillus subtilis
- Molecule
- Ribonuclease Z
- EC
- 3.1.26.11
- UniProt
- P54548
- Ligands
- ZN, PO4
- Pockets
- 3 · best druggability 0.64
Structure
x-ray diffraction · resolution 2.1 · 2 distinct chains · 27% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonuclease Z (EC 3.1.26.11) | protein | 269 | 25% helix, 30% strand | P54548 |
| B | Ribonuclease Z (EC 3.1.26.11) | protein | 297 | 28% helix, 27% strand | P54548 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A
- PO4 · Phosphate ion · ion · chains A
- GOL · Glycerol · additive · 3 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 337 | 0.64 | 0.80 | 37 | PO4 |
| 2 | 219 | 0.59 | 0.80 | 33 | empty |
| 3 | 183 | 0.52 | 0.78 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 1373 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 modified (engineered).
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 P54548
- Elsewhere: RCSB PDB 1Y44 · PDBe 1Y44 · UniProt P54548
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