Research workbench
Crystal structure of CBD12 from CALX1.2
Analyse Crystal structure of CBD12 from CALX1.2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RB7
- Type
- protein
- Length
- 982 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NA/CA exchange protein
- UniProt
- Q24413
- Ligands
- CA, SO4
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NA/CA exchange protein | protein | 248 | 6% helix, 44% strand | Q24413 |
| B | NA/CA exchange protein | protein | 242 | 7% helix, 43% strand | Q24413 |
| E | NA/CA exchange protein | protein | 248 | 9% helix, 40% strand | Q24413 |
| G | NA/CA exchange protein | protein | 244 | 5% helix, 43% strand | Q24413 |
Ligands and binding sites
- CA · Calcium ion · metal · 16 copies · chains A, B, E, G
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1002 | 0.76 | 0.79 | 93 | empty |
| 2 | 954 | 0.76 | 0.78 | 94 | empty |
| 3 | 266 | 0.58 | 0.78 | 29 | empty |
| 4 | 51 | 0.51 | 0.87 | 18 | empty |
| 5 | 81 | 0.50 | 0.83 | 26 | empty |
Interfaces
3 interfaces between chains.
- A–G · 1570 Ų buried · 11 hydrogen bonds · protein-protein
- B–E · 1477 Ų buried · 12 hydrogen bonds · protein-protein
- A–E · 723 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3RB7 · Crystal structure of CBD12 from CALX1.2 · 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 3RB7 · PDBe 3RB7 · UniProt Q24413
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