Research workbench
Crystal structure of a novel sugar isomerase from E. COLI O157:H7
Analyse Crystal structure of a novel sugar isomerase from E. COLI O157:H7 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KMH
- Type
- protein
- Length
- 442 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-lyxose isomerase
- EC
- 5.3.1.15
- UniProt
- Q8X5Q7
- Ligands
- IPH, MN
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 14% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-lyxose isomerase (EC 5.3.1.15) | protein | 219 | 14% helix, 39% strand | Q8X5Q7 |
| B | D-lyxose isomerase (EC 5.3.1.15) | protein | 223 | 14% helix, 38% strand | Q8X5Q7 |
Ligands and binding sites
- IPH · Phenol · ligand · chains B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
- ACT · Acetate ion · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 127 | 0.80 | 0.98 | 35 | empty |
| 2 | 51 | 0.69 | 0.97 | 20 | IPH |
| 3 | 214 | 0.63 | 0.83 | 34 | empty |
| 4 | 110 | 0.43 | 0.77 | 18 | empty |
| 5 | 82 | 0.38 | 0.77 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1622 Ų buried · 30 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified, 1 disulfide (engineered, disulfide).
Compared structures
- 3KMH · Crystal Structure of a Novel Sugar Isomerase from E. coli O157:H7 · 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 Q8X5Q7
- Elsewhere: RCSB PDB 3KMH · PDBe 3KMH · UniProt Q8X5Q7
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