Structure of PDB 2fyc Chain D Binding Site BS01

Receptor Information

>2fyc Chain D (length=272) Species: 9913 (Bos taurus)

LTACPEESPLLVGPMLIEFNIPVDLKLVEQQNPKVKLGGRYTPMDCISPH
KVAIIIPFRNRQEHLKYWLYYLHPILQRQQLDYGIYVINQAGESMFNRAK
LLNVGFKEALKDYDYNCFVFSDVDLIPMNDHNTYRCFSQPRHISVAMDKF
GFSLPYVQYFGGVSALSKQQFLSINGFPNNYWGWGGEDDDIYNRLAFRGM
SVSRPNAVIGKTRHIRHSRDKKNEPNPQRFDRIAHTKETMLSDGLNSLTY
MVLEVQRYPLYTKITVDIGTPS

Ligand information

• Ligand ID: GDU
• InChI: InChI=1S/C15H24N2O17P2/c18-3-5-8(20)10(22)12(24)14(32-5)33-36(28,29)34-35(26,27)30-4-6-9(21)11(23)13(31-6)17-2-1-7(19)16-15(17)25/h1-2,5-6,8-14,18,20-24H,3-4H2,(H,26,27)(H,28,29)(H,16,19,25)/t5-,6-,8+,9-,10+,11-,12-,13-,14-/m1/s1
• InChIKey: HSCJRCZFDFQWRP-ABVWGUQPSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)(O)O[P@@](=O)(O)O[C@@H]3[C@@H]([C@H]([C@H]([C@H](O3)CO)O)O)O)O)O
  CACTVS 3.341: OC[CH]1O[CH](O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)N3C=CC(=O)NC3=O)[CH](O)[CH](O)[CH]1O
  CACTVS 3.341: OC[C@H]1O[C@H](O[P@@](O)(=O)O[P@@](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N3C=CC(=O)NC3=O)[C@H](O)[C@@H](O)[C@H]1O
  ACDLabs 10.04: O=P(OC1OC(C(O)C(O)C1O)CO)(O)OP(=O)(O)OCC3OC(N2C=CC(=O)NC2=O)C(O)C3O
  OpenEye OEToolkits 1.5.0: C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OC3C(C(C(C(O3)CO)O)O)O)O)O
• Formula: C15 H24 N2 O17 P2
• Name: GALACTOSE-URIDINE-5'-DIPHOSPHATE;
  UDP-D-GALACTOPYRANOSE
• ChEMBL: CHEMBL439009
• DrugBank: DB03501
• ZINC: ZINC000008551104
• PDB chain: 2fyc Chain D Residue 528

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2fyc Structural Snapshots of beta-1,4-Galactosyltransferase-I Along the Kinetic Pathway.
• Resolution: 2.0 Å
• Binding residue (original residue number in PDB): P187 F188 R189 R191 F226 R228 D252 V253 D254 G292 W314 G315 E317 H347 D350
• Binding residue (residue number reindexed from 1): P57 F58 R59 R61 F96 R98 D122 V123 D124 G162 W184 G185 E187 H217 D220
• Annotation score: 4

Enzymatic activity

• Catalytic site (original residue number in PDB): D252 D254 W314 E317 D318 H344 H347 R349
• Catalytic site (residue number reindexed from 1): D122 D124 W184 E187 D188 H214 H217 R219
• Enzyme Commision number: 2.4.1.-
  2.4.1.22: lactose synthase.
  2.4.1.275: neolactotriaosylceramide beta-1,4-galactosyltransferase.
  2.4.1.38: beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase.
  2.4.1.90: N-acetyllactosamine synthase.

Gene Ontology

Molecular Function

• GO:0016757 glycosyltransferase activity

Biological Process

• GO:0005975 carbohydrate metabolic process

External links

• PDB: RCSB:2fyc, PDBe:2fyc, PDBj:2fyc
• PDBsum: 2fyc
• PubMed: 16497331
• UniProt: P08037|B4GT1_BOVIN Beta-1,4-galactosyltransferase 1 (Gene Name=B4GALT1)