MolNFT v1 · #129446 · protein
Crystal structure of human SHIP2 phosphatase-C2
5OKM · Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2: “Crystal structure of human SHIP2 phosphatase-C2”. X-ray diffraction, 1 ligand (NO3), 20 pockets (best druggability 0.84). MolNFT v1 #129446 on GenesisL1: 3D structure…
- PDB
- 5OKM
- Type
- protein
- Length
- 3,467 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
- NO3
- Pockets
- 20 · best druggability 0.84
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 | 435 | 17% helix, 40% strand | O15357 |
| B | Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2 (EC 3.1.3.86) | protein | 442 | 16% helix, 39% strand | O15357 |
| C | Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2 (EC 3.1.3.86) | protein | 431 | 16% helix, 40% strand | O15357 |
| D | Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2 (EC 3.1.3.86) | protein | 436 | 16% helix, 40% strand | O15357 |
| E | Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2 (EC 3.1.3.86) | protein | 432 | 17% helix, 41% strand | O15357 |
| F | Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2 (EC 3.1.3.86) | protein | 433 | 16% helix, 40% strand | O15357 |
| G | Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2 (EC 3.1.3.86) | protein | 431 | 16% helix, 39% strand | O15357 |
| H | Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2 (EC 3.1.3.86) | protein | 427 | 16% helix, 40% strand | O15357 |
Ligands and binding sites
- NO3 · Nitrate ion · ion · 2 copies · chains A, B, C, H
- EDO · 1,2-ethanediol · additive · 21 copies · chains A, D, B, H, C, F, 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 | 1010 | 0.84 | 0.85 | 117 | empty |
| 2 | 996 | 0.81 | 0.82 | 86 | empty |
| 3 | 567 | 0.78 | 0.85 | 62 | NO3 |
| 4 | 636 | 0.78 | 0.84 | 80 | empty |
| 5 | 773 | 0.77 | 0.81 | 93 | EDO |
Interfaces
12 interfaces between chains.
- D–F · 1292 Ų buried · 34 hydrogen bonds · protein-protein
- B–H · 1274 Ų buried · 35 hydrogen bonds · protein-protein
- E–F · 1028 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 899 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 807 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
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 5OKM · PDBe 5OKM · UniProt O15357
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