MolNFT v1 · #133421 · protein
INPP5D pandda analysis group deposition -- crystal structure of the phosphatase and C2 domains of SHIP1 in complex with Z1374778753
5RY8 · Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1: “INPP5D pandda analysis group deposition -- crystal structure of the phosphatase and C2 domains of SHIP1 in…”. X-ray diffraction, 3 ligands (B1J, MN, PO4), 3 pockets (best…
- PDB
- 5RY8
- Type
- protein
- Length
- 460 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- 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
- B1J, MN, PO4
- Pockets
- 3 · best druggability 0.67
Structure
x-ray diffraction · 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
- B1J · [1-(4-chlorophenyl)-1,2,3-triazol-4-yl]methanol · ligand · chains A
- MN · Manganese (II) ion · metal · chains A
- PO4 · Phosphate ion · ion · chains A
- DMS · Dimethyl sulfoxide · additive · 3 copies · chains A
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 388 | 0.67 | 0.80 | 53 | DMS |
| 2 | 88 | 0.43 | 0.79 | 23 | DMS |
| 3 | 101 | 0.36 | 0.75 | 24 | empty |
Compared structures
- 5RY8 · 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
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 5RY8 · PDBe 5RY8 · UniProt Q92835
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