Research workbench
Crystal structure of a putative sugar-phosphate isomerase (LMOF2365_0531) from listeria monocytogenes str. 4B F2365 at 1.60 a resolution
Analyse Crystal structure of a putative sugar-phosphate isomerase (LMOF2365_0531) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FXA
- Type
- protein
- Length
- 766 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sis domain protein
- UniProt
- Q723E8
- Pockets
- 7 · best druggability 0.88
Structure
x-ray diffraction · 3 distinct chains · 54% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sis domain protein | protein | 192 | 54% helix, 11% strand | Q723E8 |
| B, D | Sis domain protein | protein | 191 | 54% helix, 12% strand | Q723E8 |
| C | Sis domain protein | protein | 192 | 54% helix, 12% strand | Q723E8 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 2 copies · chains B, A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 771 | 0.88 | 0.91 | 63 | empty |
| 2 | 189 | 0.57 | 0.80 | 34 | empty |
| 3 | 204 | 0.56 | 0.79 | 34 | empty |
| 4 | 195 | 0.55 | 0.79 | 33 | empty |
| 5 | 183 | 0.54 | 0.79 | 35 | EDO |
Interfaces
6 interfaces between chains.
- C–D · 2669 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 2668 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 1078 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 1062 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 450 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 3FXA · Crystal structure of a putative sugar-phosphate isomerase (lmof2365_0531) from listeria… · 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 Q723E8
- Elsewhere: RCSB PDB 3FXA · PDBe 3FXA · UniProt Q723E8
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