MolNFT v1 · #62262 · protein
Crystal structure of calx-CBD1
3EAD · NA/CA exchange protein: “Crystal structure of calx-CBD1”. X-ray diffraction, 1 ligand (CA), 4 pockets (best druggability 0.80). MolNFT v1 #62262 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3EAD
- Type
- protein
- Length
- 448 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NA/CA exchange protein
- UniProt
- Q24413
- Ligands
- CA
- Pockets
- 4 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 3% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | NA/CA exchange protein | protein | 111 | 3% helix, 53% strand | Q24413 |
| B | NA/CA exchange protein | protein | 114 | 3% helix, 52% strand | Q24413 |
| C | NA/CA exchange protein | protein | 112 | 3% helix, 54% strand | Q24413 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 903 | 0.80 | 0.82 | 73 | GOL |
| 2 | 59 | 0.32 | 0.77 | 17 | empty |
| 3 | 69 | 0.31 | 0.74 | 16 | empty |
| 4 | 54 | 0.26 | 0.73 | 16 | empty |
Interfaces
5 interfaces between chains.
- A–C · 538 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 496 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 326 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 318 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 128 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3EAD · Crystal structure of CALX-CBD1 · 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 3EAD · PDBe 3EAD · UniProt Q24413
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