MolNFT v1 · #72480 · protein
Crystal structure of INPP5B
3N9V · Type II inositol-1,4,5-trisphosphate 5-phosphatase: “Crystal structure of INPP5B”. X-ray diffraction, 2 ligands (MG, CA), 3 pockets (best druggability 0.80). MolNFT v1 #72480 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3N9V
- Type
- protein
- Length
- 589 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type II inositol-1,4,5-trisphosphate 5-phosphatase
- EC
- 3.1.3.36
- UniProt
- P32019
- Ligands
- MG, CA
- Pockets
- 3 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Type II inositol-1,4,5-trisphosphate 5-phosphatase (EC 3.1.3.36) | protein | 300 | 22% helix, 35% strand | P32019 |
| B | Type II inositol-1,4,5-trisphosphate 5-phosphatase (EC 3.1.3.36) | protein | 289 | 23% helix, 36% strand | P32019 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · 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 | 739 | 0.80 | 0.83 | 65 | empty |
| 2 | 81 | 0.49 | 0.83 | 14 | empty |
| 3 | 51 | 0.33 | 0.78 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 627 Ų buried · 4 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 P32019
- Elsewhere: RCSB PDB 3N9V · PDBe 3N9V · UniProt P32019
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