Research workbench
Crystal structure of escherichia COLI RNase D, an exoribonuclease involved in structured RNA processing
Analyse Crystal structure of escherichia COLI RNase D, an exoribonuclease involved in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YT3
- Type
- protein
- Length
- 375 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease D
- EC
- 3.1.26.3
- UniProt
- P09155
- Ligands
- ZN, SO4
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 58% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonuclease D (EC 3.1.26.3) | protein | 375 | 58% helix, 8% strand | P09155 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 681 | 0.66 | 0.75 | 63 | SO4 |
| 2 | 234 | 0.54 | 0.77 | 27 | ZN |
| 3 | 101 | 0.44 | 0.78 | 21 | SO4 |
| 4 | 51 | 0.29 | 0.75 | 11 | empty |
Compared structures
- 1YT3 · Crystal Structure of Escherichia coli RNase D, an exoribonuclease involved in structured… · the same entry in another collection · chain A against A, TM-score 1.00
- P09155 · AlphaFold monomer V2.0 prediction for ribonuclease D (P09155) · 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 P09155
- Elsewhere: RCSB PDB 1YT3 · PDBe 1YT3 · UniProt P09155
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