Structure of PDB 6bw5 Chain A Binding Site BS01

Receptor Information

>6bw5 Chain A (length=378) Species: 9606 (Homo sapiens)

PMPLLINLIVSLLGFVATVTLIPAFRGHFIAARLCGQDLNKTSRQQIPES
QGVISGAVFLIILFCFIPFPFLNCAFPHHEFVALIGALLAICCMIFLGFA
DDVLNLRWRHKLLLPTAASLPLLMVYFTNFGNTTIHLDLGILYYVYMGLL
AVFCTNAINILAGINGLEAGQSLVISASIIVFNLVELEGDCRDDHVFSLY
FMIPFFFTTLGLLYHNWYPSRVFVGDTFCYFAGMTFAVVGILGHFSKTML
LFFMPQVFNFLYSLPQLLHIIPCPRHRIPRLNIKTGKLEMSYSKFKTKSL
SFLGTFILKVAESLQLVTVHQSETEDGEFTECNNMTLINLLLKVLGPIHE
RNLTLLLLLLQILGSAITFSIRYQLVRL

Ligand information

• Ligand ID: TUM
• InChI: InChI=1S/C37H60N4O16/c1-18(2)12-10-8-6-4-5-7-9-11-13-23(45)39-26-30(50)27(47)21(54-36(26)57-35-25(38-19(3)43)29(49)28(48)22(17-42)55-35)16-20(44)33-31(51)32(52)34(56-33)41-15-14-24(46)40-37(41)53/h11,13-15,18,20-22,25-36,42,44,47-52H,4-10,12,16-17H2,1-3H3,(H,38,43)(H,39,45)(H,40,46,53)/t20-,21-,22-,25-,26-,27+,28-,29-,30-,31+,32-,33-,34-,35-,36+/m1/s1
• InChIKey: YJQCOFNZVFGCAF-DCSBULBVSA-N
• SMILES:
  CACTVS 3.385: CC(C)CCCCCCCCC=CC(=O)N[CH]1[CH](O)[CH](O)[CH](C[CH](O)[CH]2O[CH]([CH](O)[CH]2O)N3C=CC(=O)NC3=O)O[CH]1O[CH]4O[CH](CO)[CH](O)[CH](O)[CH]4NC(C)=O
  OpenEye OEToolkits 2.0.4: CC(C)CCCCCCCCC=CC(=O)NC1C(C(C(OC1OC2C(C(C(C(O2)CO)O)O)NC(=O)C)CC(C3C(C(C(O3)N4C=CC(=O)NC4=O)O)O)O)O)O
  OpenEye OEToolkits 2.0.4: CC(C)CCCCCCCCC=CC(=O)N[C@@H]1[C@H]([C@H]([C@H](O[C@H]1O[C@@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CO)O)O)NC(=O)C)C[C@H]([C@@H]3[C@H]([C@H]([C@@H](O3)N4C=CC(=O)NC4=O)O)O)O)O)O
  ACDLabs 12.01: [C@H](C(=O)NC1C(OC(C(C1O)O)CC(C2OC(C(O)C2O)N3C(NC(C=C3)=O)=O)O)OC4OC(CO)C(O)C(O)C4NC(C)=O)=CCCCCCCCCC(C)C
  CACTVS 3.385: CC(C)CCCCCCCCC=CC(=O)N[C@@H]1[C@@H](O)[C@@H](O)[C@@H](C[C@@H](O)[C@H]2O[C@H]([C@H](O)[C@@H]2O)N3C=CC(=O)NC3=O)O[C@H]1O[C@H]4O[C@H](CO)[C@@H](O)[C@H](O)[C@H]4NC(C)=O
• Formula: C37 H60 N4 O16
• Name: Tunicamycin
• PDB chain: 6bw5 Chain A Residue 501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6bw5 GlcNAc-1-P-transferase-tunicamycin complex structure reveals basis for inhibition of N-glycosylation.
• Resolution: 3.1 Å
• Binding residue (original residue number in PDB): L46 N119 W122 K125 L126 F179 N182 N185 A188 G189 I190 N191 F249 D252 H302 R303
• Binding residue (residue number reindexed from 1): L39 N105 W108 K111 L112 F153 N156 N159 A162 G163 I164 N165 F223 D226 H276 R277
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=8.25,Kd=5.6nM

Enzymatic activity

• Enzyme Commision number: 2.7.8.15: UDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase.

Gene Ontology

Molecular Function

• GO:0003975 UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase activity
• GO:0003976 UDP-N-acetylglucosamine-lysosomal-enzyme N-acetylglucosaminephosphotransferase activity
• GO:0005515 protein binding
• GO:0016757 glycosyltransferase activity
• GO:0016780 phosphotransferase activity, for other substituted phosphate groups
• GO:0042802 identical protein binding
• GO:0046872 metal ion binding

Biological Process

• GO:0006047 UDP-N-acetylglucosamine metabolic process
• GO:0006486 protein glycosylation
• GO:0006487 protein N-linked glycosylation
• GO:0006488 dolichol-linked oligosaccharide biosynthetic process
• GO:0019348 dolichol metabolic process

Cellular Component

• GO:0005783 endoplasmic reticulum
• GO:0005789 endoplasmic reticulum membrane
• GO:0016020 membrane
• GO:0043231 intracellular membrane-bounded organelle

External links

• PDB: RCSB:6bw5, PDBe:6bw5, PDBj:6bw5
• PDBsum: 6bw5
• PubMed: 29459785
• UniProt: Q9H3H5|GPT_HUMAN UDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase (Gene Name=DPAGT1)