Structure of PDB 2d7i Chain A Binding Site BS02

Receptor Information
>2d7i Chain A (length=536) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GQKLKDWHDKEAIRRDAQRVGNGEQGRPYPMTDAERVDQAYRENGFNIYV
SDKISLNRSLPDIRHPNCNSKRYLETLPNTSIIIPFHNEGWSSLLRTVHS
VLNRSPPELVAEIVLVDDFSDREHLKKPLEDYMALFPSVRILRTKKREGL
IRTRMLGASVATGDVITFLDSHCEANVNWLPPLLDRIARNRKTIVCPMID
VIDHDDFRYETQAGDAMRGAFDWEMYYKRIPIPPELQKADPSDPFESPVM
AGGLFAVDRKWFWELGGYDPGLEIWGGEQYEISFKVWMCGGRMEDIPCSR
VGHIYRKYVPYKVPAGVSLARNLKRVAEVWMDEYAEYIYQRRPEYRHLSA
GDVAVQKKLRSSLNCKSFKWFMTKIAWDLPKFYPPVEPPAAAWGEIRNVG
TGLCADTKHGALGSPLRLEGCVRGRGEAAWNNMQVFTFTWREDIRPGDPQ
HTKKFCFDAISHTSPVTLYDCHSMKGNQLWKYRKDKTLYHPVSGSCMDCS
ESDHRIFMNTCNPSSLTQQWLFEHTNSTVLEKFNRN
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 chain2d7i Chain A Residue 705 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB2d7i Structural basis of carbohydrate transfer activity by human UDP-GalNAc: polypeptide alpha-N-acetylgalactosaminyltransferase (pp-GalNAc-T10)
Resolution2.5 Å
Binding residue
(original residue number in PDB)		F153 H154 E156 D185 R214 G216 L217 D237 S238 H239 W342 H370 R373 Y378
Binding residue
(residue number reindexed from 1)		F86 H87 E89 D118 R147 G149 L150 D170 S171 H172 W275 H303 R306 Y311
Annotation score3
Enzymatic activity
Enzyme Commision number 2.4.1.41: polypeptide N-acetylgalactosaminyltransferase.
Gene Ontology
Molecular Function
GO:0004653 polypeptide N-acetylgalactosaminyltransferase activity
GO:0016757 glycosyltransferase activity
GO:0030246 carbohydrate binding
GO:0046872 metal ion binding
Biological Process
GO:0006486 protein glycosylation
GO:0006493 protein O-linked glycosylation
GO:0016266 O-glycan processing
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:2d7i, PDBe:2d7i, PDBj:2d7i
PDBsum2d7i
PubMed16650853
UniProtQ86SR1|GLT10_HUMAN Polypeptide N-acetylgalactosaminyltransferase 10 (Gene Name=GALNT10)

[Back to BioLiP]