Structure of PDB 3ryk Chain A Binding Site BS01

Receptor Information

>3ryk Chain A (length=175) Species: 198094 (Bacillus anthracis str. Ames)

AMKVIETNFTDAKLLEPRLFGDDRGFFTESYNKKVLETLGVTHSFVQDNV
SYSAEAGTIRGLHFQKNPKAQTKLIQVMQGAIYDVIVDLRKDSPTFKQWR
GYILSADNHRQLLVPKGFAHGFCTLVPHTIVMYKVDEYYSADHDSGVLWN
DKELAIPWPVTSPILSDKDRILPLL

Ligand information

• Ligand ID: POP
• InChI: InChI=1S/H4O7P2/c1-8(2,3)7-9(4,5)6/h(H2,1,2,3)(H2,4,5,6)/p-2
• InChIKey: XPPKVPWEQAFLFU-UHFFFAOYSA-L
• SMILES:
  OpenEye OEToolkits 1.5.0: O[P@@](=O)([O-])O[P@@](=O)(O)[O-]
  CACTVS 3.341: O[P]([O-])(=O)O[P](O)([O-])=O
  ACDLabs 10.04: [O-]P(=O)(O)OP([O-])(=O)O
  OpenEye OEToolkits 1.5.0: OP(=O)([O-])OP(=O)(O)[O-]
• Formula: H2 O7 P2
• Name: PYROPHOSPHATE 2-
• PDB chain: 3ryk Chain A Residue 182

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3ryk Structure of the Bacillus anthracis dTDP-L-rhamnose-biosynthetic enzyme dTDP-4-dehydrorhamnose 3,5-epimerase (RfbC).
• Resolution: 1.631 Å
• Binding residue (original residue number in PDB): S165 K167 D168
• Binding residue (residue number reindexed from 1): S166 K168 D169
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): H62 K72 Y132 D168
• Catalytic site (residue number reindexed from 1): H63 K73 Y133 D169
• Enzyme Commision number: 5.1.3.13: dTDP-4-dehydrorhamnose 3,5-epimerase.

Gene Ontology

Molecular Function

• GO:0008830 dTDP-4-dehydrorhamnose 3,5-epimerase activity
• GO:0016853 isomerase activity
• GO:0051213 dioxygenase activity

Biological Process

• GO:0019305 dTDP-rhamnose biosynthetic process
• GO:0045226 extracellular polysaccharide biosynthetic process

Cellular Component

• GO:0005829 cytosol

External links

• PDB: RCSB:3ryk, PDBe:3ryk, PDBj:3ryk
• PDBsum: 3ryk
• PubMed: 29199987
• UniProt: A0A6L7H6N0