Research workbench
Crystal structure of calcium binding domain CBD12 of CALX1.1
Analyse Crystal structure of calcium binding domain CBD12 of CALX1.1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RB5
- Type
- protein
- Length
- 483 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NA/CA exchange protein
- UniProt
- Q24413
- Ligands
- CA, SO4
- Pockets
- 7 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NA/CA exchange protein | protein | 238 | 7% helix, 44% strand | Q24413 |
| B | NA/CA exchange protein | protein | 245 | 8% helix, 46% strand | Q24413 |
Ligands and binding sites
- CA · Calcium ion · metal · 8 copies · chains A, B
- SO4 · Sulfate ion · ion · 7 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 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 | 351 | 0.57 | 0.76 | 38 | MPD |
| 2 | 302 | 0.53 | 0.74 | 26 | empty |
| 3 | 272 | 0.51 | 0.74 | 29 | empty |
| 4 | 149 | 0.47 | 0.77 | 28 | empty |
| 5 | 87 | 0.47 | 0.80 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 587 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3RB5 · Crystal structure of calcium binding domain CBD12 of CALX1.1 · the same entry in another collection · chain A against A, 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 Q24413
- Elsewhere: RCSB PDB 3RB5 · PDBe 3RB5 · UniProt Q24413
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