Structure of PDB 1s2d Chain A Binding Site BS02

Receptor Information

>1s2d Chain A (length=165) Species: 1587 (Lactobacillus helveticus)

MKAVVPTGKIYLGSPFYSDAQRERAAKAKELLAKNPSIAHVFFPFDGFTD
PDEKPEIGGIRSMVWRDATYQNDLTGISNATCGVFLYDMDQLDDGSAFEI
GFMRAMHKPVILVPFTEHPEKEKKMNLMIAQGVTTIIDGNTEFEKLADYN
FNECPSNPVRGYGIY

Ligand information

• Ligand ID: V3M
• InChI: InChI=1S/C5H9FO4/c6-3-4(8)2(1-7)10-5(3)9/h2-5,7-9H,1H2/t2-,3+,4-,5+/m1/s1
• InChIKey: RTUWTJAKZMHWBQ-LECHCGJUSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: C([C@@H]1[C@H]([C@@H]([C@H](O1)O)F)O)O
  CACTVS 3.385: OC[C@H]1O[C@H](O)[C@@H](F)[C@@H]1O
  OpenEye OEToolkits 2.0.7: C(C1C(C(C(O1)O)F)O)O
  CACTVS 3.385: OC[CH]1O[CH](O)[CH](F)[CH]1O
  ACDLabs 12.01: OC1OC(CO)C(C1F)O
• Formula: C5 H9 F O4
• Name: 2-deoxy-2-fluoro-alpha-D-arabinofuranose
• ZINC: ZINC000044154413
• PDB chain: 1s2d Chain A Residue 202

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1s2d Structures of purine 2'-deoxyribosyltransferase, substrate complexes, and the ribosylated enzyme intermediate at 2.0 A resolution.
• Resolution: 2.1 Å
• Binding residue (original residue number in PDB): G13 S14 Y17 P44 D75 D95 G97 E101
• Binding residue (residue number reindexed from 1): G13 S14 Y17 P44 D73 D93 G95 E99
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): Y11 D75 D95 E101
• Catalytic site (residue number reindexed from 1): Y11 D73 D93 E99
• Enzyme Commision number: 2.4.2.6: nucleoside deoxyribosyltransferase.

Gene Ontology

Molecular Function

• GO:0016757 glycosyltransferase activity
• GO:0050144 nucleoside deoxyribosyltransferase activity

External links

• PDB: RCSB:1s2d, PDBe:1s2d, PDBj:1s2d
• PDBsum: 1s2d
• PubMed: 14992575
• UniProt: Q8RLY5