Research workbench
Crystal structure of cam-peptide complex containing azf at position 108
Analyse Crystal structure of cam-peptide complex containing azf at position 108 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HCS
- Type
- protein
- Length
- 628 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Calmodulin-1; CALCIUM/CALMODULIN-dependent protein kinase type II subunit beta
- EC
- 2.7.11.17
- UniProt
- P0DP23, P08413
- Ligands
- CA
- Pockets
- 9 · best druggability 0.63
Structure
x-ray diffraction · 6 distinct chains · 61% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Calmodulin-1 | protein | 137 | 60% helix, 4% strand | P0DP23 |
| B | CALCIUM/CALMODULIN-dependent protein kinase type II subunit beta (EC 2.7.11.17) | protein | 19 | 79% helix, 0% strand | P08413 |
| C | Calmodulin-1 | protein | 139 | 59% helix, 4% strand | P0DP23 |
| D | CALCIUM/CALMODULIN-dependent protein kinase type II subunit beta (EC 2.7.11.17) | protein | 21 | 71% helix, 0% strand | P08413 |
| E, G | Calmodulin-1 | protein | 138 | 56% helix, 6% strand | P0DP23 |
| F, H | CALCIUM/CALMODULIN-dependent protein kinase type II subunit beta (EC 2.7.11.17) | protein | 18 | 83% helix, 0% strand | P08413 |
Ligands and binding sites
- CA · Calcium ion · metal · 16 copies · chains A, C, E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 63 | 0.63 | 0.91 | 16 | empty |
| 2 | 192 | 0.60 | 0.81 | 31 | empty |
| 3 | 64 | 0.60 | 0.89 | 14 | empty |
| 4 | 285 | 0.55 | 0.76 | 43 | empty |
| 5 | 104 | 0.39 | 0.76 | 20 | empty |
Interfaces
11 interfaces between chains.
- C–D · 1596 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1470 Ų buried · 14 hydrogen bonds · protein-protein
- G–H · 1330 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 1328 Ų buried · 9 hydrogen bonds · protein-protein
- C–E · 661 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nonstandard).
Compared structures
- 6HCS · Crystal structure of CaM-peptide complex containing AzF at position 108 · the same entry in another collection · chain H against H, TM-score 1.00
- P08413 · AlphaFold monomer V2.0 prediction for CALCIUM/CALMODULIN-dependent protein kinase type II… · a predicted model of the same protein · chain F against A, TM-score 0.68
- P0DP23 · AlphaFold monomer V2.0 prediction for calmodulin-1 (P0DP23) · a predicted model of the same protein · chain G 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 P0DP23
- Every structure of UniProt P08413
- Elsewhere: RCSB PDB 6HCS · PDBe 6HCS · UniProt P0DP23 · UniProt P08413
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