Human inositol 1,4,5-trisphosphate 3-kinase A (IP3K) catalytic domain in complex with DL-6-deoxy-6-hydroxy-methyl-scyllo-inositol 1,2,4-trisphosphate/ATP/Mn. Determined by X-ray diffraction at 1.77 Å resolution. Released 28 Feb 2024.
Explore 8PPD in 3D Show helices and sheets RCSB PDB PDBe
8PPD contains 26 α-helices and 24 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 198-200 | 3 | 1 |
| β-strand | 206-210 | 5 | 1 |
| α-helix | 213-222 | 10 | |
| α-helix | 226-230 | 5 | |
| β-strand | 234-240 | 7 | 1 |
| β-strand | 243-249 | 7 | 1 |
| β-strand | 259-265 | 7 | 2 |
| α-helix | 273-280 | 8 | |
| β-strand | 285 | 1 | 3 |
| α-helix | 286-295 | 10 | |
| α-helix | 302-307 | 6 | |
| β-strand | 310 | 1 | 3 |
| α-helix | 312-322 | 11 | |
| α-helix | 325-328 | 4 | |
| β-strand | 330-336 | 7 | 2 |
| β-strand | 342-343 | 2 | 2 |
| α-helix | 352-363 | 12 | |
| α-helix | 367-386 | 20 | |
| α-helix | 388-391 | 4 | |
| β-strand | 393-394 | 2 | 4 |
| β-strand | 399-404 | 6 | 2 |
| β-strand | 410-415 | 6 | 2 |
| β-strand | 421-422 | 2 | 4 |
| α-helix | 423 | 1 | |
| α-helix | 434-435 | 2 | |
| α-helix | 444-459 | 16 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | 185-191 | 7 | |
| β-strand | 198-200 | 3 | 5 |
| β-strand | 206-210 | 5 | 5 |
| α-helix | 213-222 | 10 | |
| α-helix | 226-230 | 5 | |
| β-strand | 234-240 | 7 | 5 |
| β-strand | 243-249 | 7 | 5 |
| β-strand | 259-265 | 7 | 2 |
| α-helix | 272-274 | 3 | |
| α-helix | 289-295 | 7 | |
| α-helix | 312-322 | 11 | |
| α-helix | 325-328 | 4 | |
| β-strand | 330-336 | 7 | 2 |
| β-strand | 342-343 | 2 | 2 |
| α-helix | 352-363 | 12 | |
| α-helix | 367-386 | 20 | |
| α-helix | 388-391 | 4 | |
| β-strand | 393-396 | 4 | 6 |
| β-strand | 399-404 | 6 | 2 |
| β-strand | 410-415 | 6 | 2 |
| β-strand | 419-422 | 4 | 6 |
| α-helix | 423 | 1 | |
| α-helix | 434-435 | 2 | |
| α-helix | 444-460 | 17 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Inositol-trisphosphate 3-kinase A | A, B | protein | 279 | Homo sapiens | P23677 (AlphaFold model) |
>8PPD_1 Inositol-trisphosphate 3-kinase A (chains A, B) GSHMSWVQLAGHTGSFKAAGTSGLILKRCSEPERYCLARLMADALRGCVPAFHGVVERDG ESYLQLQDLLDGFDGPCVLDCKMGVRTYLEEELTKARERPKLRKDMYKKMLAVDPEAPTE EEHAQRAVTKPRYMQWREGISSSTTLGFRIEGIKKADGSCSTDFKTTRSREQVLRVFEEF VQGDEEVLRRYLNRLQQIRDTLEVSEFFRRHEVIGSSLLFVHDHCHRAGVWLIDFGKTTP LPDGQILDHRRPWEEGNREDGYLLGLDNLIGILASLAER
| ID | Name | Formula | Copies |
|---|---|---|---|
| MN | Manganese (II) ion | Mn | 2 |
| 75I | DL-6-deoxy-6-hydroxy-methyl-scyllo-inositol 1,2,4-trisphosphate | C7 H17 O15 P3 | 2 |
| ATP | Adenosine-5'-triphosphate | C10 H16 N5 O13 P3 | 2 |
Water and common crystallization additives (SO4) are not listed.
Substrate promiscuity of inositol 1,4,5-trisphosphate kinase driven by structurally-modified ligands and active site plasticity. Marquez-Monino, M.A., Ortega-Garcia, R., Whitfield, H. et al. Nat Commun (2024) 15:1502-1502. DOI 10.1038/s41467-024-45917-5 · PubMed
Other PDB entries of the same protein (UniProt P23677 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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