MolNFT v1 · #14155 · protein + DNA
Residues involved in the catalysis and base specificity of cytotoxic ribonuclease from bullfrog (rana catesbeiana)
1M07 · 5'-D(*AP*CP*GP*A)-3': “Residues involved in the catalysis and base specificity of cytotoxic ribonuclease from bullfrog (rana…”. X-ray diffraction, 1 pocket (best druggability 0.64). MolNFT v1 #14155 on GenesisL1: 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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