Research workbench
The structure of a D-lyxose isomerase from the sigmab regulon of bacillus subtilis
Analyse The structure of a D-lyxose isomerase from the sigmab regulon of bacillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Y0O
- Type
- protein
- Length
- 171 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable D-lyxose ketol-isomerase
- EC
- 5.3.1.15
- UniProt
- P96578
- Ligands
- ZN, ARS, SO4
- Pockets
- 1 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 15% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable D-lyxose ketol-isomerase (EC 5.3.1.15) | protein | 171 | 15% helix, 40% strand | P96578 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A
- ARS · Arsenic · metal · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 59 | 0.63 | 0.93 | 21 | ARS |
Modifications
Observed in the structure: 2 modified (engineered).
Compared structures
- 2Y0O · The structure of a D-lyxose isomerase from the sigmaB regulon of Bacillus subtilis · the same entry in another collection · chain A against A, TM-score 1.00
- P96578 · AlphaFold monomer V2.0 prediction for probable D-lyxose ketol- isomerase (P96578) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P96578
- Elsewhere: RCSB PDB 2Y0O · PDBe 2Y0O · UniProt P96578
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