MolNFT v1 · #62242 · protein
Crystal structure of apo-form calx CBD1 domain
3E9T · NA/CA exchange protein: “Crystal structure of apo-form calx CBD1 domain”. X-ray diffraction, 1 ligand (CA), 2 pockets (best druggability 0.73). MolNFT v1 #62242 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3E9T
- Type
- protein
- Length
- 433 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
- 2 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 0% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NA/CA exchange protein | protein | 112 | 0% helix, 55% strand | Q24413 |
| B | NA/CA exchange protein | protein | 113 | 0% helix, 55% strand | Q24413 |
| C | NA/CA exchange protein | protein | 105 | 0% helix, 58% strand | Q24413 |
| D | NA/CA exchange protein | protein | 103 | 0% helix, 54% strand | Q24413 |
Ligands and binding sites
- CA · Calcium ion · metal · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 775 | 0.73 | 0.78 | 60 | empty |
| 2 | 77 | 0.32 | 0.73 | 13 | empty |
Interfaces
4 interfaces between chains.
- A–C · 636 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 361 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 284 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 157 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3E9T · Crystal structure of Apo-form Calx CBD1 domain · 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 3E9T · PDBe 3E9T · UniProt Q24413
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