Research workbench
Residues involved in the catalysis and base specificity of cytotoxic ribonuclease from bullfrog (rana catesbeiana)
Analyse Residues involved in the catalysis and base specificity of cytotoxic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1M07
- Type
- protein + DNA
- Length
- 230 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*AP*CP*GP*A)-3'; Ribonuclease
- EC
- 3.1.27.5
- UniProt
- P11916
- Pockets
- 1 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D | 5'-D(*AP*CP*GP*A)-3' | dna | 4 | — | — |
| A, B | Ribonuclease (EC 3.1.27.5) | protein | 111 | 21% helix, 42% strand | P11916 |
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 539 | 0.64 | 0.76 | 44 | empty |
Interfaces
5 interfaces between chains.
- C–A · 453 Ų buried · 17 hydrogen bonds · protein-nucleic
- D–B · 436 Ų buried · 14 hydrogen bonds · protein-nucleic
- D–A · 186 Ų buried · 6 hydrogen bonds · protein-nucleic
- C–B · 166 Ų buried · 2 hydrogen bonds · protein-nucleic
- C–D · 146 Ų buried · 6 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 8 disulfide, 2 modified (disulfide, cyclization).
Compared structures
- 1M07 · Residues involved in the catalysis and base specificity of cytotoxic ribonuclease from… · the same entry in another collection · chain C against C, TM-score 1.00
- P11916 · AlphaFold monomer V2.0 prediction for oocytes ribonuclease (P11916) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P11916
- Elsewhere: RCSB PDB 1M07 · PDBe 1M07 · UniProt P11916
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