Research workbench
Crystal structure of the golgi casein kinase with MN/ADP bound
Analyse Crystal structure of the golgi casein kinase with MN/ADP bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KQB
- Type
- protein
- Length
- 837 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein H03A11.1
- UniProt
- Q9XTW2
- Ligands
- ADP, NAG, MAN, MN, NI
- Pockets
- 8 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein H03A11.1 | protein | 419 | 35% helix, 15% strand | Q9XTW2 |
| B | Protein H03A11.1 | protein | 418 | 35% helix, 15% strand | Q9XTW2 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains B
- MN · Manganese (II) ion · metal · 4 copies · chains A, B
- NI · Nickel (II) ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1022 | 0.76 | 0.79 | 96 | MN, ADP |
| 2 | 425 | 0.67 | 0.80 | 41 | MN, ADP |
| 3 | 130 | 0.59 | 0.85 | 29 | empty |
| 4 | 125 | 0.56 | 0.84 | 29 | empty |
| 5 | 129 | 0.46 | 0.78 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 316 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 4KQB · crystal structure of the Golgi casein kinase with Mn/ADP bound · the same entry in another collection · chain A against A, TM-score 1.00
- Q9XTW2 · AlphaFold monomer V2.0 prediction for extracellular SERINE/THREONINE protein kinase… · a predicted model of the same protein · chain B against A, 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 Q9XTW2
- Elsewhere: RCSB PDB 4KQB · PDBe 4KQB · UniProt Q9XTW2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.