Research workbench
Cocrystal structure of human camkii-alpha (CAMK2A)KINASE domain and GLUN2B(S1303D)
Analyse Cocrystal structure of human camkii-alpha (CAMK2A)KINASE domain and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KL1
- Type
- protein
- Length
- 564 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CALCIUM/CALMODULIN-dependent protein kinase type II subunit alpha; Glutamate receptor…
- EC
- 2.7.11.17
- UniProt
- Q9UQM7, Q13224
- Ligands
- ATP, MG
- Pockets
- 6 · best druggability 0.88
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | CALCIUM/CALMODULIN-dependent protein kinase type II subunit alpha (EC 2.7.11.17) | protein | 268 | 40% helix, 21% strand | Q9UQM7 |
| C | Glutamate receptor ionotropic, NMDA 2B | protein | 15 | 0% helix, 7% strand | Q13224 |
| D | Glutamate receptor ionotropic, NMDA 2B | protein | 13 | 0% helix, 15% strand | Q13224 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1034 | 0.88 | 0.89 | 114 | MG, EDO, ATP |
| 2 | 302 | 0.62 | 0.79 | 36 | empty |
| 3 | 93 | 0.56 | 0.85 | 20 | empty |
| 4 | 114 | 0.53 | 0.82 | 16 | EDO |
| 5 | 83 | 0.38 | 0.77 | 23 | empty |
Interfaces
6 interfaces between chains.
- B–D · 1062 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 986 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 446 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 368 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 322 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7KL1 · Cocrystal structure of human CaMKII-alpha (CAMK2A)kinase domain and GluN2B(S1303D) · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UQM7 · AlphaFold monomer V2.0 prediction for CALCIUM/CALMODULIN-dependent protein kinase type II… · a predicted model of the same protein · chain A against A, TM-score 0.95
- Q13224 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, NMDA 2B (Q13224) · a predicted model of the same protein · chain D against A, TM-score 0.37
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 Q9UQM7
- Every structure of UniProt Q13224
- Elsewhere: RCSB PDB 7KL1 · PDBe 7KL1 · UniProt Q9UQM7 · UniProt Q13224
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