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Structure of the tetradecameric oligomerisation domain of calcium- calmodulin dependent protein kinase II delta
Analyse Structure of the tetradecameric oligomerisation domain of calcium- calmodulin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2W2C
- Type
- protein
- Length
- 1,787 residues
- Chains
- 14
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CALCIUM/CALMODULIN-dependent protein kinase type II delta chain
- EC
- 2.7.11.17
- UniProt
- Q13557
- Ligands
- CD
- Pockets
- 20 · best druggability 0.64
Structure
x-ray diffraction · 12 distinct chains · 33% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CALCIUM/CALMODULIN-dependent protein kinase type II delta chain (EC 2.7.11.17) | protein | 128 | 34% helix, 47% strand | Q13557 |
| B | CALCIUM/CALMODULIN-dependent protein kinase type II delta chain (EC 2.7.11.17) | protein | 128 | 33% helix, 47% strand | Q13557 |
| C, G | CALCIUM/CALMODULIN-dependent protein kinase type II delta chain (EC 2.7.11.17) | protein | 127 | 31% helix, 46% strand | Q13557 |
| D, J | CALCIUM/CALMODULIN-dependent protein kinase type II delta chain (EC 2.7.11.17) | protein | 125 | 32% helix, 49% strand | Q13557 |
| E | CALCIUM/CALMODULIN-dependent protein kinase type II delta chain (EC 2.7.11.17) | protein | 129 | 34% helix, 47% strand | Q13557 |
| F | CALCIUM/CALMODULIN-dependent protein kinase type II delta chain (EC 2.7.11.17) | protein | 126 | 33% helix, 48% strand | Q13557 |
| H | CALCIUM/CALMODULIN-dependent protein kinase type II delta chain (EC 2.7.11.17) | protein | 131 | 33% helix, 45% strand | Q13557 |
| I | CALCIUM/CALMODULIN-dependent protein kinase type II delta chain (EC 2.7.11.17) | protein | 128 | 34% helix, 48% strand | Q13557 |
| K | CALCIUM/CALMODULIN-dependent protein kinase type II delta chain (EC 2.7.11.17) | protein | 127 | 30% helix, 47% strand | Q13557 |
| L | CALCIUM/CALMODULIN-dependent protein kinase type II delta chain (EC 2.7.11.17) | protein | 130 | 32% helix, 47% strand | Q13557 |
| M | CALCIUM/CALMODULIN-dependent protein kinase type II delta chain (EC 2.7.11.17) | protein | 125 | 31% helix, 48% strand | Q13557 |
| N | CALCIUM/CALMODULIN-dependent protein kinase type II delta chain (EC 2.7.11.17) | protein | 131 | 35% helix, 47% strand | Q13557 |
Ligands and binding sites
- CD · Cadmium ion · metal · 6 copies · chains B, F, H, J
- ACT · Acetate ion · additive · 14 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 431 | 0.64 | 0.77 | 30 | ACT |
| 2 | 373 | 0.64 | 0.78 | 28 | ACT |
| 3 | 402 | 0.63 | 0.77 | 29 | ACT |
| 4 | 327 | 0.62 | 0.78 | 24 | ACT |
| 5 | 323 | 0.62 | 0.78 | 28 | ACT |
Interfaces
35 interfaces between chains.
- A–K · 1163 Ų buried · 14 hydrogen bonds · protein-protein
- E–H · 1158 Ų buried · 16 hydrogen bonds · protein-protein
- B–L · 1151 Ų buried · 14 hydrogen bonds · protein-protein
- G–M · 1149 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1147 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 2W2C · Structure of the tetradecameric oligomerisation domain of calcium- calmodulin dependent… · the same entry in another collection · chain K against K, 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 Q13557
- Elsewhere: RCSB PDB 2W2C · PDBe 2W2C · UniProt Q13557
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