MolNFT v1 · #122827 · protein
Crystal structure of inositol monophosphate bound saimpase-II
5J16 · Inositol monophosphatase family protein: “Crystal structure of inositol monophosphate bound saimpase-II”. X-ray diffraction, 3 ligands (IPD, CA, PO4), 14 pockets (best druggability 0.71). MolNFT v1 #122827 on GenesisL1: 3D…
- PDB
- 5J16
- Type
- protein
- Length
- 1,019 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inositol monophosphatase family protein
- UniProt
- A0A1I9GET0
- Ligands
- IPD, CA, PO4
- Pockets
- 14 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Inositol monophosphatase family protein | protein | 258 | 43% helix, 26% strand | A0A1I9GET0 |
| B | Inositol monophosphatase family protein | protein | 254 | 44% helix, 25% strand | A0A1I9GET0 |
| C | Inositol monophosphatase family protein | protein | 253 | 43% helix, 25% strand | A0A1I9GET0 |
| D | Inositol monophosphatase family protein | protein | 254 | 46% helix, 25% strand | A0A1I9GET0 |
Ligands and binding sites
- IPD · D-myo-inositol-1-phosphate · ligand · 3 copies · chains A, B, C
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 587 | 0.71 | 0.79 | 59 | empty |
| 2 | 594 | 0.70 | 0.79 | 52 | empty |
| 3 | 285 | 0.58 | 0.78 | 30 | CA, IPD |
| 4 | 288 | 0.57 | 0.77 | 31 | CA, PO4 |
| 5 | 273 | 0.57 | 0.78 | 32 | IPD |
Interfaces
3 interfaces between chains.
- A–D · 1265 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 1237 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 113 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5J16 · Crystal structure of Inositol monophosphate bound SaIMPase-II · 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 A0A1I9GET0
- Elsewhere: RCSB PDB 5J16 · PDBe 5J16 · UniProt A0A1I9GET0
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