MolNFT v1 · #65168 · protein
Calmodulin bound to peptide from calmodulin kinase II (camkii)
3GP2: “Calmodulin bound to peptide from calmodulin kinase II (camkii)”. X-ray diffraction, 3 ligands (ACE, CA, NH2), 2 pockets (best druggability 0.36). MolNFT v1 #65168 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3GP2
- Type
- protein
- Length
- 166 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Calmodulin; CALCIUM/CALMODULIN-dependent protein kinase type II delta chain
- EC
- 2.7.11.17
- UniProt
- P62149, Q13557
- Ligands
- ACE, CA, NH2
- Pockets
- 2 · best druggability 0.36
Structure
x-ray diffraction · 2 distinct chains · 61% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Calmodulin | protein | 146 | 60% helix, 4% strand | P62149 |
| B | CALCIUM/CALMODULIN-dependent protein kinase type II delta chain (EC 2.7.11.17) | protein | 20 | 75% helix, 0% strand | Q13557 |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains B
- CA · Calcium ion · metal · 4 copies · chains A
- NH2 · Amino group · ion · 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 61 | 0.36 | 0.78 | 11 | empty |
| 2 | 78 | 0.35 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1443 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 3GP2 · Calmodulin bound to peptide from calmodulin kinase II (CaMKII) · the same entry in another collection · chain A against A, TM-score 1.00
- Q13557 · AlphaFold monomer V2.0 prediction for CALCIUM/CALMODULIN-dependent protein kinase type II… · a predicted model of the same protein · chain B against A, TM-score 0.60
- P62149 · AlphaFold monomer V2.0 prediction for calmodulin (P62149) · a predicted model of the same protein · chain A against A, TM-score 0.52
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 P62149
- Every structure of UniProt Q13557
- Elsewhere: RCSB PDB 3GP2 · PDBe 3GP2 · UniProt P62149 · UniProt Q13557
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