Structure of PDB 6wmn Chain D Binding Site BS02

Receptor Information
>6wmn Chain D (length=302) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AYWNREQEKLNRQYNPILISHLNYCEPDLRVTSVVTGFNNLPDRFKDFLL
YLRCRNYSLLIDQPDKCAKKPFLLLAIKSLTPHFARRQAIRESWGQESNQ
TVVRVFLLGQTPPEDNHPDLSDMLKFESEKHQDILMWNYRDTFFNLSLKE
VLFLRWVSTSCPDTEFVFKGDDDVFVNTHHILNYLNSLSKTKAKDLFIGD
VIHNAGPHRDKKLKYYIPEVVYSGLYPPYAGGGGFLYSGHLALRLYHITD
QVHLYPIDDVYTGMCLQKLGLVPEKHKGFRTFDIEEKMLVHSRKPQEMID
IW
Ligand information
Ligand IDUDP
InChIInChI=1S/C9H14N2O12P2/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(22-8)3-21-25(19,20)23-24(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
InChIKeyXCCTYIAWTASOJW-XVFCMESISA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)(O)OP(=O)(O)O)O)O
CACTVS 3.370O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
CACTVS 3.370O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
OpenEye OEToolkits 1.7.0C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)O)O)O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)C(O)C2O
FormulaC9 H14 N2 O12 P2
NameURIDINE-5'-DIPHOSPHATE
ChEMBLCHEMBL130266
DrugBankDB03435
ZINCZINC000004490939
PDB chain6wmn Chain D Residue 402 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6wmn Comparison of human poly-N-acetyl-lactosamine synthase structure with GT-A fold glycosyltransferases supports a modular assembly of catalytic subsites.
Resolution2.04 Å
Binding residue
(original residue number in PDB)		K149 S150 L151 H154 D215 T216 F217 L220 K223 D245 D246 K288 Y289 H376
Binding residue
(residue number reindexed from 1)		K78 S79 L80 H83 D141 T142 F143 L146 K149 D171 D172 K214 Y215 H291
Annotation score3
Enzymatic activity
Enzyme Commision number 2.4.1.149: N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase.
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0008499 UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity
GO:0008532 N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase activity
GO:0016757 glycosyltransferase activity
GO:0016758 hexosyltransferase activity
Biological Process
GO:0006486 protein glycosylation
GO:0006493 protein O-linked glycosylation
GO:0007411 axon guidance
GO:0007608 sensory perception of smell
GO:0016266 O-glycan processing
GO:0018146 keratan sulfate biosynthetic process
GO:0030311 poly-N-acetyllactosamine biosynthetic process
GO:1990830 cellular response to leukemia inhibitory factor
Cellular Component
GO:0000139 Golgi membrane
GO:0005794 Golgi apparatus
GO:0016020 membrane

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6wmn, PDBe:6wmn, PDBj:6wmn
PDBsum6wmn
PubMed33229435
UniProtQ9NY97|B3GN2_HUMAN N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase 2 (Gene Name=B3GNT2)

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