Research workbench
NMR-based model of the complex of the toxin kid and a 5-nucleotide substrate RNA fragment (auaca)
Analyse NMR-based model of the complex of the toxin kid and a 5-nucleotide substrate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2C06
- Type
- protein + RNA
- Length
- 225 residues
- Chains
- 3
- Method
- solution nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kid toxin protein; 5'-R(*AP*UP*AP*CP*AP)-3'
- UniProt
- P13976
- Pockets
- 1 · best druggability 0.69
Structure
solution nmr · 2 distinct chains · 15% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Kid toxin protein | protein | 110 | 15% helix, 22% strand | P13976 |
| C | 5'-R(*AP*UP*AP*CP*AP)-3' | rna | 5 | — | — |
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 | 59 | 0.69 | 0.96 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1252 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 621 Ų buried · 33 hydrogen bonds · protein-nucleic
- B–C · 186 Ų buried · 3 hydrogen bonds · protein-nucleic
Compared structures
- 2C06 · NMR-based model of the complex of the toxin Kid and a 5-nucleotide substrate RNA fragment… · the same entry in another collection · chain A against A, TM-score 1.00
- P13976 · AlphaFold monomer V2.0 prediction for endoribonuclease pemk (P13976) · a predicted model of the same protein · chain A against A, TM-score 0.85
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 P13976
- Elsewhere: RCSB PDB 2C06 · PDBe 2C06 · UniProt P13976
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