Research workbench
CDPK1, from toxoplasma gondii, bound to inhibitory vhh-1B7
Analyse CDPK1, from toxoplasma gondii, bound to inhibitory vhh-1B7 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YGA
- Type
- protein
- Length
- 2,279 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Calmodulin-domain protein kinase 1; Vhh-1B7
- UniProt
- Q9BJF5
- Ligands
- CA
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · 6 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Calmodulin-domain protein kinase 1 | protein | 448 | 46% helix, 13% strand | Q9BJF5 |
| B | Vhh-1B7 | protein | 124 | 2% helix, 48% strand | — |
| C | Calmodulin-domain protein kinase 1 | protein | 449 | 45% helix, 12% strand | Q9BJF5 |
| D, F, H | Vhh-1B7 | protein | 123 | 2% helix, 48% strand | — |
| E | Calmodulin-domain protein kinase 1 | protein | 442 | 47% helix, 13% strand | Q9BJF5 |
| G | Calmodulin-domain protein kinase 1 | protein | 447 | 47% helix, 12% strand | Q9BJF5 |
Ligands and binding sites
- CA · Calcium ion · metal · 16 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 959 | 0.72 | 0.76 | 79 | empty |
| 2 | 162 | 0.71 | 0.90 | 35 | empty |
| 3 | 390 | 0.69 | 0.81 | 46 | empty |
| 4 | 176 | 0.63 | 0.84 | 30 | empty |
| 5 | 478 | 0.63 | 0.76 | 59 | empty |
Interfaces
9 interfaces between chains.
- C–D · 865 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 848 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 843 Ų buried · 13 hydrogen bonds · protein-protein
- G–H · 797 Ų buried · 12 hydrogen bonds · protein-protein
- E–G · 671 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 4YGA · CDPK1, from Toxoplasma gondii, bound to inhibitory VHH-1B7 · 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 Q9BJF5
- Elsewhere: RCSB PDB 4YGA · PDBe 4YGA · UniProt Q9BJF5
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