Research workbench
Crystal structure of the clic homologue exc-4 from C. elegans
Analyse Crystal structure of the clic homologue exc-4 from C. elegans in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YV9
- Type
- protein
- Length
- 551 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chloride intracellular channel exc-4
- UniProt
- Q8WQA4
- Ligands
- CA
- Pockets
- 5 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 57% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chloride intracellular channel exc-4 | protein | 285 | 55% helix, 8% strand | Q8WQA4 |
| B | Chloride intracellular channel exc-4 | protein | 266 | 59% helix, 9% strand | Q8WQA4 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1016 | 0.86 | 0.87 | 100 | CA |
| 2 | 60 | 0.36 | 0.79 | 17 | empty |
| 3 | 91 | 0.34 | 0.74 | 19 | empty |
| 4 | 56 | 0.30 | 0.75 | 14 | empty |
| 5 | 59 | 0.30 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1421 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 2YV9 · Crystal structure of the CLIC homologue EXC-4 from c. elegans · the same entry in another collection · chain B against B, TM-score 1.00
- Q8WQA4 · AlphaFold monomer V2.0 prediction for chloride intracellular channel exc-4 (Q8WQA4) · 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 Q8WQA4
- Elsewhere: RCSB PDB 2YV9 · PDBe 2YV9 · UniProt Q8WQA4
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