Research workbench
Inositol 1,3,4,5,6-pentakisphosphate 2-kinase from M. musculus in complex with ATP and IP5
Analyse Inositol 1,3,4,5,6-pentakisphosphate 2-kinase from M. musculus in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MWL
- Type
- protein
- Length
- 815 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inositol-pentakisphosphate 2-kinase
- EC
- 2.7.1.158
- UniProt
- Q6P1C1
- Ligands
- ATP, 5MY, ZN, MG
- Pockets
- 9 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Inositol-pentakisphosphate 2-kinase (EC 2.7.1.158) | protein | 421 | 40% helix, 15% strand | Q6P1C1 |
| B | Inositol-pentakisphosphate 2-kinase (EC 2.7.1.158) | protein | 394 | 42% helix, 15% strand | Q6P1C1 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · chains A
- 5MY · Myo-inositol-(1,3,4,5,6)-pentakisphosphate · ligand · chains A
- ZN · Zinc ion · metal · 4 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 749 | 0.82 | 0.86 | 73 | ATP, 5MY, MG |
| 2 | 658 | 0.77 | 0.83 | 73 | empty |
| 3 | 54 | 0.71 | 0.98 | 18 | empty |
| 4 | 231 | 0.58 | 0.79 | 29 | empty |
| 5 | 117 | 0.55 | 0.83 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 842 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5MWL · INOSITOL 1,3,4,5,6-PENTAKISPHOSPHATE 2-KINASE FROM M. MUSCULUS IN COMPLEX WITH ATP and IP5 · the same entry in another collection · chain A against A, TM-score 1.00
- Q6P1C1 · AlphaFold monomer V2.0 prediction for inositol-pentakisphosphate 2-kinase (Q6P1C1) · 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 Q6P1C1
- Elsewhere: RCSB PDB 5MWL · PDBe 5MWL · UniProt Q6P1C1
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