Research workbench
1.75 ångström crystal structure of the N53I ca-CAM:CAV1.2 iq domain complex
Analyse 1.75 ångström crystal structure of the N53I ca-CAM:CAV1.2 iq domain complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6U3D
- Type
- protein
- Length
- 349 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Calmodulin-1; Voltage-dependent L-type calcium channel subunit alpha-1C
- UniProt
- P0DP23, Q13936
- Ligands
- CA
- Pockets
- 3 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 67% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Calmodulin-1 | protein | 146 | 61% helix, 5% strand | P0DP23 |
| C | Voltage-dependent L-type calcium channel subunit alpha-1C | protein | 28 | 89% helix, 0% strand | Q13936 |
| D | Voltage-dependent L-type calcium channel subunit alpha-1C | protein | 29 | 72% helix, 0% strand | Q13936 |
Ligands and binding sites
- CA · Calcium ion · metal · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 655 | 0.76 | 0.82 | 75 | empty |
| 2 | 101 | 0.37 | 0.75 | 21 | empty |
| 3 | 56 | 0.30 | 0.75 | 17 | empty |
Interfaces
5 interfaces between chains.
- B–D · 1594 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 1529 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 474 Ų buried · 9 hydrogen bonds · protein-protein
- C–B · 97 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 22 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6U3D · 1.75 Angstrom crystal structure of the N53I Ca-CaM:CaV1.2 IQ domain complex · the same entry in another collection · chain D against D, TM-score 1.00
- Q13936 · AlphaFold monomer V2.0 prediction for voltage-dependent L-type calcium channel subunit… · a predicted model of the same protein · chain C against A, TM-score 0.78
- P0DP23 · AlphaFold monomer V2.0 prediction for calmodulin-1 (P0DP23) · a predicted model of the same protein · chain B against A, TM-score 0.51
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 P0DP23
- Every structure of UniProt Q13936
- Elsewhere: RCSB PDB 6U3D · PDBe 6U3D · UniProt P0DP23 · UniProt Q13936
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