Structure of PDB 2agd Chain B Binding Site BS02

Receptor Information

>2agd Chain B (length=273) Species: 9606 (Homo sapiens)

SLPACPEESPLLVGPMLIEFNMPVDLELVAKQNPNVKMGGRYAPRDCVSP
HKVAIIIPFRNRQEHLKYWLYYLHPVLQRQQLDYGIYVINQAGDTIFNRA
KLLNVGFQEALKDYDYTCFVFSDVDLIPMNDHNAYRCFSQPRHISVAMDK
FGFSLPYVQYFGGVSALSKQQFLTINGFPNNYWGWGGEDDDIFNRLVFRG
MSISRPNAVVGTTRHIRHSRDKKNEPNPQRFDRIAHTKETMLSDGLNSLT
YQVLDVQRYPLYTQITVDIGTPS

Ligand information

• Ligand ID: UDH
• InChI: InChI=1S/C15H27N3O12P2/c16-6-3-1-2-4-8-27-31(23,24)30-32(25,26)28-9-10-12(20)13(21)14(29-10)18-7-5-11(19)17-15(18)22/h5,7,10,12-14,20-21H,1-4,6,8-9,16H2,(H,23,24)(H,25,26)(H,17,19,22)/t10-,12-,13-,14-/m1/s1
• InChIKey: MLWJBKPFDKRHBM-FMKGYKFTSA-N
• SMILES:
  OpenEye OEToolkits 1.7.5: C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OCCCCCCN)O)O
  ACDLabs 10.04: O=P(O)(OCCCCCCN)OP(=O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)C(O)C2O
  OpenEye OEToolkits 1.7.5: C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)(O)O[P@@](=O)(O)OCCCCCCN)O)O
  CACTVS 3.385: NCCCCCCO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)N2C=CC(=O)NC2=O
  CACTVS 3.385: NCCCCCCO[P](O)(=O)O[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N2C=CC(=O)NC2=O
• Formula: C15 H27 N3 O12 P2
• Name: 6-AMINOHEXYL-URIDINE-C1,5'-DIPHOSPHATE
• DrugBank: DB02696
• ZINC: ZINC000013523996
• PDB chain: 2agd Chain B Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2agd Oligosaccharide Preferences of beta1,4-Galactosyltransferase-I: Crystal Structures of Met340His Mutant of Human beta1,4-Galactosyltransferase-I with a Pentasaccharide and Trisaccharides of the N-Glycan Moiety
• Resolution: 1.9 Å
• Binding residue (original residue number in PDB): P183 F184 R185 R187 F222 D248 V249 D250 K275 W310 H343 R345 D346
• Binding residue (residue number reindexed from 1): P58 F59 R60 R62 F97 D123 V124 D125 K150 W185 H218 R220 D221
• Annotation score: 2

Enzymatic activity

• Catalytic site (original residue number in PDB): D248 D250 W310 E313 D314 H340 H343 R345
• Catalytic site (residue number reindexed from 1): D123 D125 W185 E188 D189 H215 H218 R220
• 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:2agd, PDBe:2agd, PDBj:2agd
• PDBsum: 2agd
• PubMed: 16157350
• UniProt: P15291|B4GT1_HUMAN Beta-1,4-galactosyltransferase 1 (Gene Name=B4GALT1)