Research workbench
Crystal structure of SCCK2 alpha in complex with gmppnp
Analyse Crystal structure of SCCK2 alpha in complex with gmppnp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LFI
- Type
- protein
- Length
- 741 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Casein kinase II subunit alpha
- EC
- 2.7.11.1
- UniProt
- P15790
- Ligands
- GNP, MN, SO4
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Casein kinase II subunit alpha (EC 2.7.11.1) | protein | 370 | 42% helix, 14% strand | P15790 |
| B | Casein kinase II subunit alpha (EC 2.7.11.1) | protein | 371 | 43% helix, 14% strand | P15790 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 10 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
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 | 1159 | 0.82 | 0.83 | 118 | GNP, MN, GOL |
| 2 | 334 | 0.69 | 0.83 | 42 | GNP, MN, GOL |
| 3 | 146 | 0.56 | 0.82 | 23 | empty |
| 4 | 134 | 0.54 | 0.81 | 20 | empty |
| 5 | 61 | 0.37 | 0.79 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 519 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
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 P15790
- Elsewhere: RCSB PDB 4LFI · PDBe 4LFI · UniProt P15790
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