Research workbench
Crystal structure of AKAP79 calmodulin binding domain peptide in complex with CA2+/CALMODULIN
Analyse Crystal structure of AKAP79 calmodulin binding domain peptide in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NIN
- Type
- protein
- Length
- 305 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Calmodulin; A-kinase anchor protein 5
- UniProt
- P62158, P24588
- Ligands
- CA, SO4
- Pockets
- 3 · best druggability 0.44
Structure
x-ray diffraction · 3 distinct chains · 61% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Calmodulin | protein | 141 | 62% helix, 7% strand | P62158 |
| A | Calmodulin | protein | 142 | 61% helix, 7% strand | P62158 |
| C, D | A-kinase anchor protein 5 | protein | 11 | 45% helix, 0% strand | P24588 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 55 | 0.44 | 0.84 | 15 | empty |
| 2 | 69 | 0.39 | 0.79 | 16 | empty |
| 3 | 59 | 0.30 | 0.75 | 15 | empty |
Interfaces
3 interfaces between chains.
- B–D · 850 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 820 Ų buried · 10 hydrogen bonds · protein-protein
- B–A · 789 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5NIN · Crystal Structure of AKAP79 calmodulin binding domain peptide in complex with… · the same entry in another collection · chain B against B, TM-score 1.00
- P24588 · AlphaFold monomer V2.0 prediction for a-kinase anchor protein 5 (P24588) · a predicted model of the same protein · chain C against A, TM-score 0.54
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 P62158
- Every structure of UniProt P24588
- Elsewhere: RCSB PDB 5NIN · PDBe 5NIN · UniProt P62158 · UniProt P24588
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