Research workbench
Structural and functional characterization of a calcium-activated cation channel from tsukamurella paurometabola
Analyse Structural and functional characterization of a calcium-activated cation… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CBF
- Type
- protein
- Length
- 612 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ion transport 2 domain protein
- UniProt
- D5UM26
- Ligands
- CA
- Pockets
- 8 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 67% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Ion transport 2 domain protein | protein | 102 | 67% helix, 0% strand | D5UM26 |
Ligands and binding sites
- CA · Calcium ion · metal · 3 copies · chains A, E, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 529 | 0.73 | 0.82 | 75 | CA |
| 2 | 237 | 0.55 | 0.77 | 23 | empty |
| 3 | 213 | 0.54 | 0.77 | 21 | empty |
| 4 | 197 | 0.52 | 0.76 | 19 | empty |
| 5 | 205 | 0.52 | 0.76 | 24 | empty |
Interfaces
8 interfaces between chains.
- A–E · 1219 Ų buried · 3 hydrogen bonds · protein-protein
- D–E · 1173 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 1151 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 1085 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 181 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5CBF · Structural and Functional Characterization of a Calcium-activated Cation channel from… · the same entry in another collection · chain F against F, TM-score 1.00
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 D5UM26
- Elsewhere: RCSB PDB 5CBF · PDBe 5CBF · UniProt D5UM26
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