MolNFT v1 · #63744 · protein
Crystal structure of putative phosphosugar isomerase (YP_167080.1) from silicibacter pomeroyi dss-3 at 1.75 a resolution
3FJ1: “Crystal structure of putative phosphosugar isomerase (YP_167080.1) from silicibacter pomeroyi dss-3 at 1.75 a…”. X-ray diffraction, 1 ligand (CL), 8 pockets (best druggability 0.81). MolNFT v1 #63744 on GenesisL1: 3D structure…
- PDB
- 3FJ1
- Type
- protein
- Length
- 1,319 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative phosphosugar isomerase
- UniProt
- Q5LSC5
- Ligands
- CL
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 52% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative phosphosugar isomerase | protein | 332 | 52% helix, 13% strand | Q5LSC5 |
| B | Putative phosphosugar isomerase | protein | 328 | 53% helix, 13% strand | Q5LSC5 |
| C | Putative phosphosugar isomerase | protein | 327 | 51% helix, 13% strand | Q5LSC5 |
| D | Putative phosphosugar isomerase | protein | 332 | 52% helix, 13% strand | Q5LSC5 |
Ligands and binding sites
- CL · Chloride ion · ion · 11 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1128 | 0.81 | 0.83 | 111 | CL, EDO |
| 2 | 932 | 0.81 | 0.83 | 86 | CL |
| 3 | 584 | 0.71 | 0.79 | 68 | empty |
| 4 | 96 | 0.54 | 0.84 | 26 | CL |
| 5 | 98 | 0.53 | 0.83 | 24 | CL |
Interfaces
4 interfaces between chains.
- C–D · 1851 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1844 Ų buried · 22 hydrogen bonds · protein-protein
- B–D · 349 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 100 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 22 modified (engineered).
Compared structures
- 3FJ1 · Crystal structure of putative phosphosugar isomerase (YP_167080.1) from SILICIBACTER… · 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 Q5LSC5
- Elsewhere: RCSB PDB 3FJ1 · PDBe 3FJ1 · UniProt Q5LSC5
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