Research workbench
Crystal structure of the calcium sensor calcium-binding protein 1 (CABP1)
Analyse Crystal structure of the calcium sensor calcium-binding protein 1 (CABP1) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OX5
- Type
- protein
- Length
- 918 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Calcium-binding protein 1
- UniProt
- Q9NZU7
- Ligands
- CA
- Pockets
- 16 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 64% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Calcium-binding protein 1 | protein | 153 | 64% helix, 3% strand | Q9NZU7 |
Ligands and binding sites
- CA · Calcium ion · metal · 12 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 774 | 0.80 | 0.83 | 66 | empty |
| 2 | 472 | 0.79 | 0.87 | 63 | empty |
| 3 | 638 | 0.77 | 0.83 | 80 | empty |
| 4 | 311 | 0.74 | 0.86 | 29 | empty |
| 5 | 306 | 0.71 | 0.85 | 28 | empty |
Interfaces
12 interfaces between chains.
- C–D · 1637 Ų buried · 29 hydrogen bonds · protein-protein
- E–F · 1611 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1502 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 844 Ų buried · 12 hydrogen bonds · protein-protein
- A–E · 833 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 3OX5 · Crystal Structure of the calcium sensor calcium-binding protein 1 (CaBP1) · the same entry in another collection · chain F against F, TM-score 1.00
- Q9NZU7 · AlphaFold monomer V2.0 prediction for calcium-binding protein 1 (Q9NZU7) · a predicted model of the same protein · chain A against A, TM-score 0.78
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 Q9NZU7
- Elsewhere: RCSB PDB 3OX5 · PDBe 3OX5 · UniProt Q9NZU7
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