MolNFT v1 · #28927 · protein
Crystal structure of escherichia COLI RNase D, an exoribonuclease involved in structured RNA processing
1YT3 · Ribonuclease D: “Crystal structure of escherichia COLI RNase D, an exoribonuclease involved in structured RNA processing”. X-ray diffraction, 2 ligands (ZN, SO4), 4 pockets (best druggability 0.66). MolNFT v1 #28927 on GenesisL1: 3D…
- 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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