Research workbench
C. elegans CLP1 bound to ssrna dinucleotide gc, AMP-pnp, and MG2+(INHIBITED substrate bound state)
Analyse C. elegans CLP1 bound to ssrna dinucleotide gc, AMP-pnp, and MG2+(INHIBITED… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4OHY
- Type
- protein + RNA
- Length
- 400 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein clpf-1; RNA (5'-R(*GP*C)-3')
- UniProt
- P52874
- Ligands
- ANP, MG
- Pockets
- 3 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein clpf-1 | protein | 398 | 28% helix, 33% strand | P52874 |
| B | RNA (5'-R(*GP*C)-3') | rna | 2 | — | — |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains A, B
- MG · Magnesium ion · metal · chains A
- 2PE · Nonaethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1181 | 0.80 | 0.82 | 103 | ANP, MG |
| 2 | 84 | 0.42 | 0.79 | 14 | empty |
| 3 | 58 | 0.35 | 0.78 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 326 Ų buried · 12 hydrogen bonds · protein-nucleic
Compared structures
- 4OHY · C. Elegans Clp1 bound to ssRNA dinucleotide GC, AMP-PNP, and Mg2+(inhibited substrate… · the same entry in another collection · chain A against A, TM-score 1.00
- P52874 · AlphaFold monomer V2.0 prediction for protein clpf-1 (P52874) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P52874
- Elsewhere: RCSB PDB 4OHY · PDBe 4OHY · UniProt P52874
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