Research workbench
Crystal structure of PIP4KIIBETA complex with gmppnp
Analyse Crystal structure of PIP4KIIBETA 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
- 3X04
- Type
- protein
- Length
- 611 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphatidylinositol 5-phosphate 4-kinase type-2 beta
- EC
- 2.7.1.149
- UniProt
- P78356
- Ligands
- GNP
- Pockets
- 8 · best druggability 0.65
Structure
x-ray diffraction · 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 | 314 | 38% helix, 22% strand | P78356 |
| B | Phosphatidylinositol 5-phosphate 4-kinase type-2 beta (EC 2.7.1.149) | protein | 297 | 35% helix, 24% strand | P78356 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 315 | 0.65 | 0.80 | 41 | GNP |
| 2 | 280 | 0.62 | 0.80 | 37 | GNP |
| 3 | 102 | 0.45 | 0.79 | 20 | empty |
| 4 | 111 | 0.43 | 0.77 | 21 | empty |
| 5 | 83 | 0.43 | 0.80 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1343 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 3X04 · Crystal structure of PIP4KIIBETA complex with GMPPNP · 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 3X04 · PDBe 3X04 · UniProt P78356
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