Research workbench
Crystal structure of the PI5P4Kbeta-AMPPNP complex
Analyse Crystal structure of the PI5P4Kbeta-AMPPNP complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6K4H
- Type
- protein
- Length
- 620 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.55
- Source
- Homo sapiens
- Molecule
- Phosphatidylinositol 5-phosphate 4-kinase type-2 beta
- EC
- 2.7.1.149
- UniProt
- P78356
- Ligands
- ANP
- Pockets
- 10 · best druggability 0.65
Structure
x-ray diffraction · resolution 2.55 · 2 distinct chains · 36% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphatidylinositol 5-phosphate 4-kinase type-2 beta (EC 2.7.1.149) | protein | 319 | 37% helix, 22% strand | P78356 |
| B | Phosphatidylinositol 5-phosphate 4-kinase type-2 beta (EC 2.7.1.149) | protein | 301 | 36% helix, 23% strand | P78356 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 169 | 0.65 | 0.86 | 42 | empty |
| 2 | 310 | 0.63 | 0.80 | 45 | ANP |
| 3 | 349 | 0.62 | 0.78 | 41 | ANP |
| 4 | 110 | 0.51 | 0.82 | 26 | empty |
| 5 | 124 | 0.48 | 0.79 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1345 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 6K4H · Crystal structure of the PI5P4KBETA-amppnp complex · the same entry in another collection · chain A against A, TM-score 1.00
- P78356 · AlphaFold monomer V2.0 prediction for phosphatidylinositol 5-phosphate 4-kinase type-2… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P78356
- Elsewhere: RCSB PDB 6K4H · PDBe 6K4H · UniProt P78356
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