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Crystal structure of CRN-4-MES complex
Analyse Crystal structure of CRN-4-MES complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DK5
- Type
- protein
- Length
- 589 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.1
- Source
- Caenorhabditis elegans
- Molecule
- Cell death-related nuclease 4
- EC
- 3.1.-.-
- UniProt
- Q10905
- Ligands
- ZN, MG
- Pockets
- 7 · best druggability 0.65
Structure
x-ray diffraction · resolution 2.1 · 2 distinct chains · 37% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cell death-related nuclease 4 (EC 3.1.-.-) | protein | 294 | 37% helix, 18% strand | Q10905 |
| B | Cell death-related nuclease 4 (EC 3.1.-.-) | protein | 295 | 37% helix, 18% strand | Q10905 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- IPA · Isopropyl alcohol · additive · 7 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 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 | 436 | 0.65 | 0.78 | 50 | MES, MG, IPA |
| 2 | 398 | 0.65 | 0.78 | 43 | MES, MG |
| 3 | 114 | 0.52 | 0.81 | 18 | empty |
| 4 | 143 | 0.50 | 0.79 | 24 | empty |
| 5 | 149 | 0.46 | 0.77 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 955 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
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 5DK5 · PDBe 5DK5 · UniProt Q10905
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