Structure of PDB 5efd Chain B Binding Site BS03

Receptor Information

>5efd Chain B (length=354) Species: 65673 (Bacillus sp. NG-27)

VQPFAAQVASLADRYEESFDIGAAVEPHQLNGRQGKVLKHHYNSIVAENA
MKPISLQPEEGVFTWDGADAIVEFARKNNMNLRFHTLVWHNQVPDWFFLD
EEGNPMVEETNEAKRQANKELLLERLETHIKTVVERYKDDVTAWDVVNEV
VDDGTPNERGLRESVWYQITGDEYIRVAFETARKYAGEDAKLFINDYNTE
VTPKRDHLYNLVQDLLADGVPIDGVGHQAHIQIDWPTIDEIRTSMEMFAG
LGLDNQVTELDVSLYGWPPRPAFPTYDAIPQERFQAQADRYNQLFELYEE
LDADLSSVTFWGIADNHTWLDDRAREYNDGVGKDAPFVFDPNYRVKPAFW
RIID

Ligand information

• Ligand ID: EDO
• InChI: InChI=1S/C2H6O2/c3-1-2-4/h3-4H,1-2H2
• InChIKey: LYCAIKOWRPUZTN-UHFFFAOYSA-N
• SMILES:
  ACDLabs 10.04
  CACTVS 3.341: OCCO
  OpenEye OEToolkits 1.5.0: C(CO)O
• Formula: C2 H6 O2
• Name: 1,2-ETHANEDIOL;
  ETHYLENE GLYCOL
• ChEMBL: CHEMBL457299
• ZINC: ZINC000005224354
• PDB chain: 5efd Chain B Residue 404

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5efd Small Glycols Discover Cryptic Pockets on Proteins for Fragment-Based Approaches.
• Resolution: 1.674 Å
• Binding residue (original residue number in PDB): H230 Q232 W319 R323
• Binding residue (residue number reindexed from 1): H230 Q232 W319 R323
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): E149 N195 H230 E259 D261
• Catalytic site (residue number reindexed from 1): E149 N195 H230 E259 D261
• Enzyme Commision number: 3.2.1.8: endo-1,4-beta-xylanase.

Gene Ontology

Molecular Function

• GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds
• GO:0016798 hydrolase activity, acting on glycosyl bonds
• GO:0031176 endo-1,4-beta-xylanase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0005975 carbohydrate metabolic process
• GO:0045493 xylan catabolic process

External links

• PDB: RCSB:5efd, PDBe:5efd, PDBj:5efd
• PDBsum: 5efd
• PubMed: 33570386
• UniProt: O30700