MolNFT v1 · #129447 · protein
Crystal structure of human SHIP2 phosphatase-C2 D607A mutant
5OKN · Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2: “Crystal structure of human SHIP2 phosphatase-C2 D607A mutant”. X-ray diffraction, 2 ligands (MG, PO4), 20 pockets (best druggability 0.79). MolNFT v1 #129447 on GenesisL1…
- PDB
- 5OKN
- Type
- protein
- Length
- 3,405 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2
- EC
- 3.1.3.86
- UniProt
- O15357
- Ligands
- MG, PO4
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 8 distinct chains · 16% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2 (EC 3.1.3.86) | protein | 434 | 18% helix, 40% strand | O15357 |
| B | Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2 (EC 3.1.3.86) | protein | 431 | 15% helix, 40% strand | O15357 |
| C | Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2 (EC 3.1.3.86) | protein | 421 | 17% helix, 40% strand | O15357 |
| D | Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2 (EC 3.1.3.86) | protein | 433 | 15% helix, 40% strand | O15357 |
| E | Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2 (EC 3.1.3.86) | protein | 427 | 16% helix, 41% strand | O15357 |
| F | Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2 (EC 3.1.3.86) | protein | 427 | 17% helix, 40% strand | O15357 |
| G | Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2 (EC 3.1.3.86) | protein | 402 | 16% helix, 38% strand | O15357 |
| H | Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2 (EC 3.1.3.86) | protein | 430 | 17% helix, 40% strand | O15357 |
Ligands and binding sites
- MG · Magnesium ion · metal · 6 copies · chains C, D, E, F, G, H
- PO4 · Phosphate ion · ion · 6 copies · chains C, D, E, F, G, H
- EDO · 1,2-ethanediol · additive · 17 copies · chains A, B, H, D, F, E, G
- B3P · 2-[3-(2-hydroxy-1,1-dihydroxymethyl-ethylamino)-propylamino]-2-hydroxymethyl-propane-1,3-diol · additive · 7 copies · chains A, D, B, C, E, F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 441 | 0.79 | 0.88 | 71 | PO4, MG, EDO |
| 2 | 561 | 0.76 | 0.83 | 51 | empty |
| 3 | 470 | 0.75 | 0.84 | 53 | empty |
| 4 | 604 | 0.75 | 0.82 | 71 | EDO |
| 5 | 709 | 0.75 | 0.80 | 51 | empty |
Interfaces
12 interfaces between chains.
- D–F · 1291 Ų buried · 33 hydrogen bonds · protein-protein
- B–H · 1213 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 923 Ų buried · 17 hydrogen bonds · protein-protein
- C–H · 850 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 795 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 5OKN · Crystal structure of human SHIP2 Phosphatase-C2 D607A mutant · the same entry in another collection · chain H against H, TM-score 1.00
- O15357 · AlphaFold monomer V2.0 prediction for phosphatidylinositol 3,4,5-trisphosphate… · a predicted model of the same protein · chain H 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 O15357
- Elsewhere: RCSB PDB 5OKN · PDBe 5OKN · UniProt O15357
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