Research workbench
Crystal structure of cell-death related nuclease 4 (crn-4) bound with er
Analyse Crystal structure of cell-death related nuclease 4 (crn-4) bound with er in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CM6
- Type
- protein
- Length
- 590 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, ER3
- Pockets
- 7 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cell death-related nuclease 4 (EC 3.1.-.-) | protein | 294 | 38% helix, 18% strand | Q10905 |
| B | Cell death-related nuclease 4 (EC 3.1.-.-) | protein | 296 | 38% helix, 18% strand | Q10905 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
- ER3 · Erbium (III) 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 423 | 0.66 | 0.79 | 48 | ER3 |
| 2 | 402 | 0.66 | 0.79 | 43 | ER3 |
| 3 | 183 | 0.50 | 0.77 | 34 | empty |
| 4 | 115 | 0.49 | 0.80 | 21 | empty |
| 5 | 147 | 0.49 | 0.78 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 931 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 3CM6 · Crystal structure of cell-death related nuclease 4 (CRN-4) bound with Er · 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 0.98
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 3CM6 · PDBe 3CM6 · UniProt Q10905
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