MolNFT v1 · #56178 · protein + DNA
E.COLI RNase 1 in complex with D(CGCGATCGCG)
2Z70 · Ribonuclease I: “E.COLI RNase 1 in complex with D(CGCGATCGCG)”. X-ray diffraction, 1 ligand (CA), 2 pockets (best druggability 0.48). MolNFT v1 #56178 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2Z70
- Type
- protein + DNA
- Length
- 247 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease I; DNA (5'-D(*DCP*DGP*DCP*DGP*DAP*DTP*DCP*DGP*DCP*DG)-3')
- EC
- 3.1.27.6
- UniProt
- P21338
- Ligands
- CA
- Pockets
- 2 · best druggability 0.48
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonuclease I (EC 3.1.27.6) | protein | 245 | 43% helix, 16% strand | P21338 |
| B | DNA (5'-D(*DCP*DGP*DCP*DGP*DAP*DTP*DCP*DGP*DCP*DG)-3') | dna | 2 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 123 | 0.48 | 0.79 | 26 | empty |
| 2 | 74 | 0.34 | 0.75 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 500 Ų buried · 7 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 disulfide (disulfide).
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 P21338
- Elsewhere: RCSB PDB 2Z70 · PDBe 2Z70 · UniProt P21338
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