MolNFT v1 · #49021 · protein
Crystal structure of human inositol 1,3,4-trisphosphate 5/6-kinase (ITPK1) in complex with ADP and MN2+
2QB5 · Inositol-tetrakisphosphate 1-kinase: “Crystal structure of human inositol 1,3,4-trisphosphate 5/6-kinase (ITPK1) in complex with ADP and MN2+”. X-ray diffraction, 3 ligands (ADP, MN, SO4), 9 pockets (best druggability 0.78). MolNFT…
- PDB
- 2QB5
- Type
- protein
- Length
- 674 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inositol-tetrakisphosphate 1-kinase
- EC
- 2.7.1.134, 2.7.1.159
- UniProt
- Q13572
- Ligands
- ADP, MN, SO4
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Inositol-tetrakisphosphate 1-kinase (EC 2.7.1.134, 2.7.1.159) | protein | 338 | 36% helix, 23% strand | Q13572 |
| B | Inositol-tetrakisphosphate 1-kinase (EC 2.7.1.134, 2.7.1.159) | protein | 336 | 34% helix, 23% strand | Q13572 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 12 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 432 | 0.78 | 0.86 | 53 | SO4, MN, ADP |
| 2 | 452 | 0.78 | 0.86 | 50 | SO4, MN, ADP |
| 3 | 588 | 0.73 | 0.81 | 64 | SO4 |
| 4 | 237 | 0.62 | 0.82 | 33 | empty |
| 5 | 188 | 0.61 | 0.83 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 1895 Ų buried · 40 hydrogen bonds · protein-protein
Compared structures
- 2QB5 · Crystal Structure of Human Inositol 1,3,4-Trisphosphate 5/6-Kinase (ITPK1) in Complex… · the same entry in another collection · chain A against A, TM-score 1.00
- Q13572 · AlphaFold monomer V2.0 prediction for inositol-tetrakisphosphate 1-kinase (Q13572) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 Q13572
- Elsewhere: RCSB PDB 2QB5 · PDBe 2QB5 · UniProt Q13572
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