Research workbench
INPP5D PanDDA analysis group deposition -- Crystal Structure of the phosphatase and C2 domains of SHIP1 in complex with Z2856434898
Analyse INPP5D PanDDA analysis group deposition -- Crystal Structure of the phosphatase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5RWO
- Type
- protein
- Length
- 460 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.29
- Source
- Homo sapiens
- Molecule
- Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1
- EC
- 3.1.3.86, 3.1.3.56, 3.1.3.36
- UniProt
- Q92835
- Ligands
- AXG
- Pockets
- 5 · best druggability 0.68
Structure
x-ray diffraction · resolution 1.29 · 1 distinct chain · 17% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1 (EC 3.1.3.86, 3.1.3.56, 3.1.3.36) | protein | 460 | 17% helix, 37% strand | Q92835 |
Ligands and binding sites
- AXG · 1-(phenylmethyl)-4-pyrrol-1-yl-piperidine · ligand · chains A
- DMS · Dimethyl sulfoxide · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 387 | 0.68 | 0.81 | 49 | DMS |
| 2 | 103 | 0.45 | 0.79 | 22 | DMS |
| 3 | 98 | 0.35 | 0.75 | 19 | empty |
| 4 | 55 | 0.28 | 0.75 | 19 | empty |
| 5 | 50 | 0.28 | 0.75 | 18 | empty |
Compared structures
- 5RWO · INPP5D pandda analysis group deposition -- crystal structure of the phosphatase and C2… · the same entry in another collection · chain A against A, TM-score 1.00
- Q92835 · AlphaFold monomer V2.0 prediction for phosphatidylinositol 3,4,5-trisphosphate… · a predicted model of the same protein · chain A 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 Q92835
- Elsewhere: RCSB PDB 5RWO · PDBe 5RWO · UniProt Q92835
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