MolNFT v1 · #28934 · protein
Crystal structure of oligoribonuclease, the lone essential exoribonuclease in escherichia COLI
1YTA: “Crystal structure of oligoribonuclease, the lone essential exoribonuclease in escherichia COLI”. X-ray diffraction, 7 pockets (best druggability 0.87). MolNFT v1 #28934 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1YTA
- Type
- protein
- Length
- 720 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oligoribonuclease
- EC
- 3.1.-.-
- UniProt
- P39287
- Pockets
- 7 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Oligoribonuclease (EC 3.1.-.-) | protein | 180 | 46% helix, 17% strand | P39287 |
Ligands and binding sites
- FLC · Citrate anion · additive · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1047 | 0.87 | 0.88 | 92 | FLC |
| 2 | 213 | 0.73 | 0.89 | 37 | empty |
| 3 | 167 | 0.62 | 0.84 | 28 | empty |
| 4 | 369 | 0.60 | 0.77 | 41 | FLC |
| 5 | 343 | 0.56 | 0.75 | 37 | FLC |
Interfaces
5 interfaces between chains.
- A–B · 1816 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1797 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 667 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 276 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 212 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 1YTA · Crystal Structure of Oligoribonuclease, the lone essential exoribonuclease in Escherichia… · the same entry in another collection · 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 P39287
- Elsewhere: RCSB PDB 1YTA · PDBe 1YTA · UniProt P39287
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