Structure of PDB 8cd0 Chain A Binding Site BS02

Receptor Information
>8cd0 Chain A (length=716) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PLVLVFVESLYSQLGQEVVAILESSRFKYRTEIAPTLTDKGRGRFALIIY
ENILKYVNLDAWNRELLDKYCVAYGVGIIGFFDCSINPKSPLLYVTRPSE
VFQSNHSTYEPVLLATVVQDLGLHDGIQRVLFGNNLNFWLHKLVFVDAVA
FLTGKRLSLPLDRYILVDIDDIFVGKEGTRMKVEDVKALFDTQNELRAHI
PNFTFNLGYSGKFFHTGTNAEDAGDDLLLSYVKEFWWFPHMWSHMQPHLF
HNQSVLAEQMALNKKFAVEHGIPTDMGYAVAPHHSGVYPVHVQLYEAWKQ
VWSIRVTSTEEYPHLKPARYRRGFIHNGIMVLPRQTCGLFTHTIFYNEYP
GGSSELDKIINGGELFLTVLLNPISIFMTHLSNYGNDRLGLYTFKHLVRF
LHSWTNLRLQTLPPVQLAQKYFQIFSEEKDPLWQDPCEDKRHKDIWSKEK
TCDRFPKLLIIGPQKTGTTALYLFLGMHPDLSSNYPSSETFEEIQFFNGH
NYHKGIDWYMEFFPIPSNTTSDFYFEKSANYFDSEVAPRRAAALLPKAKV
LTILINPADRAYSWYQHQRAHDDPVALKYTFHEVISSKLRALQNRCLVPG
WYATHIERWLSAYHANQILVLDGKLLRTEPAKVMDMVQKFLGVTNTIDYH
KTLAFDPKKGFWCCLGKSKGRKYPEMDLDSRAFLKDYYRDHNIELSKLLY
KMGQTLPTWLREDLQN
Ligand information
Ligand IDCA
InChIInChI=1S/Ca/q+2
InChIKeyBHPQYMZQTOCNFJ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341[Ca++]
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Ca+2]
FormulaCa
NameCALCIUM ION
ChEMBL
DrugBankDB14577
ZINC
PDB chain8cd0 Chain A Residue 902 [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]
PDB8cd0 Structural and mechanistic characterization of bifunctional heparan sulfate N-deacetylase-N-sulfotransferase 1
Resolution2.42 Å
Binding residue
(original residue number in PDB)		D320 H389 H393
Binding residue
(residue number reindexed from 1)		D171 H240 H244
Annotation score1
Enzymatic activity
Enzyme Commision number 2.8.2.8: [heparan sulfate]-glucosamine N-sulfotransferase.
3.5.1.-
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0008146 sulfotransferase activity
GO:0015016 [heparan sulfate]-glucosamine N-sulfotransferase activity
GO:0016740 transferase activity
GO:0016787 hydrolase activity
GO:0019213 deacetylase activity
GO:0050119 N-acetylglucosamine deacetylase activity
GO:0102140 heparan sulfate N-deacetylase activity
Biological Process
GO:0000271 polysaccharide biosynthetic process
GO:0003279 cardiac septum development
GO:0006954 inflammatory response
GO:0007507 heart development
GO:0007585 respiratory gaseous exchange by respiratory system
GO:0008283 cell population proliferation
GO:0008543 fibroblast growth factor receptor signaling pathway
GO:0009887 animal organ morphogenesis
GO:0015012 heparan sulfate proteoglycan biosynthetic process
GO:0015014 heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process
GO:0015015 heparan sulfate proteoglycan biosynthetic process, enzymatic modification
GO:0030203 glycosaminoglycan metabolic process
GO:0030210 heparin biosynthetic process
GO:0030900 forebrain development
GO:0030901 midbrain development
GO:0035904 aorta development
GO:0043410 positive regulation of MAPK cascade
GO:0045880 positive regulation of smoothened signaling pathway
GO:0048702 embryonic neurocranium morphogenesis
GO:0048703 embryonic viscerocranium morphogenesis
GO:0060976 coronary vasculature development
Cellular Component
GO:0000139 Golgi membrane
GO:0005794 Golgi apparatus
GO:0016020 membrane
GO:0032588 trans-Golgi network membrane

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8cd0, PDBe:8cd0, PDBj:8cd0
PDBsum8cd0
PubMed38351061
UniProtP52848|NDST1_HUMAN Bifunctional heparan sulfate N-deacetylase/N-sulfotransferase 1 (Gene Name=NDST1)

[Back to BioLiP]