MolNFT v1 · #121721 · protein
Crystal structure of staphylococcal impase-II
5I3S · Inositol monophosphatase family protein: “Crystal structure of staphylococcal impase-II”. X-ray diffraction, 1 ligand (PO4), 15 pockets (best druggability 0.73). MolNFT v1 #121721 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5I3S
- Type
- protein
- Length
- 1,027 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inositol monophosphatase family protein
- UniProt
- A0A0J9WZD1
- Ligands
- PO4
- Pockets
- 15 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Inositol monophosphatase family protein | protein | 262 | 46% helix, 24% strand | A0A0J9WZD1 |
| B | Inositol monophosphatase family protein | protein | 258 | 45% helix, 25% strand | A0A0J9WZD1 |
| C | Inositol monophosphatase family protein | protein | 258 | 46% helix, 24% strand | A0A0J9WZD1 |
| D | Inositol monophosphatase family protein | protein | 249 | 45% helix, 25% strand | A0A0J9WZD1 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 657 | 0.73 | 0.80 | 60 | empty |
| 2 | 614 | 0.72 | 0.79 | 54 | empty |
| 3 | 293 | 0.57 | 0.77 | 31 | PO4 |
| 4 | 121 | 0.57 | 0.84 | 23 | empty |
| 5 | 267 | 0.56 | 0.78 | 31 | PO4 |
Interfaces
4 interfaces between chains.
- A–B · 1314 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 1296 Ų buried · 28 hydrogen bonds · protein-protein
- A–D · 918 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 495 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5I3S · Crystal structure of Staphylococcal IMPase-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 A0A0J9WZD1
- Elsewhere: RCSB PDB 5I3S · PDBe 5I3S · UniProt A0A0J9WZD1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.