Research workbench
Crystal structure of a human CALCIUM/CALMODULIN dependent serine protein kinase (cask) PDZ domain in complex with neurexin-1 peptide
Analyse Crystal structure of a human CALCIUM/CALMODULIN dependent serine protein kinase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NID
- Type
- protein
- Length
- 276 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peripheral plasma membrane protein cask; Neurexin-1
- EC
- 2.7.11.1
- UniProt
- O14936, Q9ULB1
- Pockets
- 2 · best druggability 0.75
Structure
x-ray diffraction · 5 distinct chains · 18% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peripheral plasma membrane protein cask (EC 2.7.11.1) | protein | 86 | 17% helix, 38% strand | O14936 |
| B | Peripheral plasma membrane protein cask (EC 2.7.11.1) | protein | 88 | 17% helix, 38% strand | O14936 |
| C | Peripheral plasma membrane protein cask (EC 2.7.11.1) | protein | 86 | 21% helix, 38% strand | O14936 |
| D | Neurexin-1 | protein | 6 | 0% helix, 33% strand | Q9ULB1 |
| E, F | Neurexin-1 | protein | 5 | 0% helix, 40% strand | Q9ULB1 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · chains 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 569 | 0.75 | 0.82 | 55 | empty |
| 2 | 86 | 0.47 | 0.81 | 24 | empty |
Interfaces
8 interfaces between chains.
- C–F · 543 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 527 Ų buried · 15 hydrogen bonds · protein-protein
- A–E · 448 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 274 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 237 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6NID · Crystal structure of a human calcium/calmodulin dependent serine protein kinase (CASK)… · the same entry in another collection · chain F against F, TM-score 1.00
- O14936 · AlphaFold monomer V2.0 prediction for peripheral plasma membrane protein cask (O14936) · a predicted model of the same protein · chain C against A, TM-score 0.96
- Q9ULB1 · AlphaFold monomer V2.0 prediction for neurexin-1 (Q9ULB1) · a predicted model of the same protein · chain E against A, TM-score 0.91
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 O14936
- Every structure of UniProt Q9ULB1
- Elsewhere: RCSB PDB 6NID · PDBe 6NID · UniProt O14936 · UniProt Q9ULB1
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