Research workbench
Crystal structure of cell-death related nuclease 4 (crn-4) bound with mn
Analyse Crystal structure of cell-death related nuclease 4 (crn-4) bound with mn in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CM5
- Type
- protein
- Length
- 588 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cell death-related nuclease 4
- EC
- 3.1.-.-
- UniProt
- Q10905
- Ligands
- ZN, MN
- Pockets
- 7 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cell death-related nuclease 4 (EC 3.1.-.-) | protein | 294 | 38% helix, 18% strand | Q10905 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 389 | 0.66 | 0.80 | 44 | MN |
| 2 | 405 | 0.65 | 0.79 | 47 | MN |
| 3 | 189 | 0.52 | 0.78 | 26 | empty |
| 4 | 107 | 0.51 | 0.82 | 21 | empty |
| 5 | 165 | 0.50 | 0.78 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 930 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 3CM5 · Crystal structure of Cell-Death Related Nuclease 4 (CRN-4) bound with Mn · the same entry in another collection · chain A against A, TM-score 1.00
- Q10905 · AlphaFold monomer V2.0 prediction for cell death-related nuclease 4 (Q10905) · a predicted model of the same protein · chain B 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 Q10905
- Elsewhere: RCSB PDB 3CM5 · PDBe 3CM5 · UniProt Q10905
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