Research workbench
Crystal structure of the PI5P4KBETA N203D-itp complex
Analyse Crystal structure of the PI5P4KBETA N203D-itp complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EM6
- Type
- protein
- Length
- 612 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
- IDP, CZU
- Pockets
- 9 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphatidylinositol 5-phosphate 4-kinase type-2 beta (EC 2.7.1.149) | protein | 316 | 36% helix, 23% strand | P78356 |
| B | Phosphatidylinositol 5-phosphate 4-kinase type-2 beta (EC 2.7.1.149) | protein | 296 | 34% helix, 24% strand | P78356 |
Ligands and binding sites
- IDP · Inosine-5'-diphosphate · ligand · 2 copies · chains A, B
- CZU · [[(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-(6-oxidanylidene-1~{H}-purin-9-yl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 243 | 0.62 | 0.81 | 35 | IDP |
| 2 | 314 | 0.62 | 0.79 | 35 | IDP |
| 3 | 179 | 0.61 | 0.83 | 38 | empty |
| 4 | 114 | 0.45 | 0.78 | 21 | empty |
| 5 | 74 | 0.42 | 0.80 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1366 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 7EM6 · Crystal structure of the PI5P4Kbeta N203D-ITP 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 7EM6 · PDBe 7EM6 · UniProt P78356
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