Research workbench
Crystal structure of PIP4KIIBETA I368A complex with gmp
Analyse Crystal structure of PIP4KIIBETA I368A complex with gmp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3X0C
- Type
- protein
- Length
- 624 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
- 5GP
- Pockets
- 9 · best druggability 0.67
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 | 319 | 38% helix, 22% strand | P78356 |
| B | Phosphatidylinositol 5-phosphate 4-kinase type-2 beta (EC 2.7.1.149) | protein | 305 | 34% helix, 24% strand | P78356 |
Ligands and binding sites
- 5GP · Guanosine-5'-monophosphate · ligand · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 358 | 0.67 | 0.81 | 46 | empty |
| 2 | 295 | 0.63 | 0.80 | 37 | 5GP |
| 3 | 155 | 0.47 | 0.77 | 29 | empty |
| 4 | 96 | 0.44 | 0.79 | 21 | empty |
| 5 | 106 | 0.42 | 0.77 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1352 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 3X0C · Crystal structure of PIP4KIIBETA I368A complex with GMP · 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 B 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 3X0C · PDBe 3X0C · UniProt P78356
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