Research workbench
Crystal structure of putative sugar isomerase (YP_050048.1) from erwinia carotovora atroseptica SCRI1043 at 1.54 a resolution
Analyse Crystal structure of putative sugar isomerase (YP_050048.1) from erwinia… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KTC
- Type
- protein
- Length
- 660 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xylose isomerase
- EC
- 5.3.1.5
- UniProt
- Q6D5T7
- Ligands
- UNL, FE, MG, CL
- Pockets
- 9 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Xylose isomerase (EC 5.3.1.5) | protein | 330 | 45% helix, 15% strand | Q6D5T7 |
Ligands and binding sites
- UNL · Unknown ligand · ligand · 3 copies · chains A, B
- FE · Fe (III) ion · metal · 4 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 15 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 426 | 0.74 | 0.84 | 59 | EDO |
| 2 | 422 | 0.65 | 0.78 | 38 | FE, UNL, EDO |
| 3 | 433 | 0.64 | 0.77 | 36 | UNL |
| 4 | 56 | 0.43 | 0.83 | 21 | EDO |
| 5 | 62 | 0.42 | 0.81 | 21 | EDO |
Interfaces
1 interface between chains.
- A–B · 2178 Ų buried · 34 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (engineered).
Compared structures
- 3KTC · Crystal structure of Putative sugar isomerase (YP_050048.1) from ERWINIA CAROTOVORA… · the same entry in another collection · chain A against A, TM-score 1.00
- Q6D5T7 · AlphaFold monomer V2.0 prediction for D-apiose isomerase (Q6D5T7) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q6D5T7
- Elsewhere: RCSB PDB 3KTC · PDBe 3KTC · UniProt Q6D5T7
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