Structure of PDB 4d0z Chain E Binding Site BS03

Receptor Information
>4d0z Chain E (length=495) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KVRWPDFNQEAYVGGTMVRSGQDPYARNKFNQVESDKLRMDRAIPDTRHD
QCQRKQWRVDLPATSVVITFHNEARSALLRTVVSVLKKSPPHLIKEIILV
DDYSNDPEDGALLGKIEKVRVLRNDRREGLMRSRVRGADAAQAKVLTFLD
SHCECNEHWLEPLLERVAEDRTRVVSPIIDVINMDNFQYVGASADLKGGF
DWNLVFKWDYMTPEQRRSRQGNPVAPIKTPMIAGGLFVMDKFYFEELGKY
DMMMDVWGGENLEISFRVWQCGGSLEIIPCSRVGHVFRKQHPYTFPGGSG
TVFARNTRRAAEVWMDEYKNFYYAAVPSARNVPYGNIQSRLELRKKLSCK
PFKWYLENVYPELRVPDHQDIAFGALQQGTNCLDTLGHFADGVVGVYECH
NAGGNQEWALTKEKSVKHMDLCLTVVDRAPGSLIKLQGCREDDSRQKWEQ
IEGNSKLRHVGSNLCLDSRTAKSGGLSVEVCGPALSQQWKFTLNL
Ligand information
Ligand IDBBK
InChIInChI=1S/C8H15NO5S/c1-3(11)9-5-7(13)6(12)4(2-10)15-8(5)14/h4-8,10,12-14H,2H2,1H3,(H,9,11)/t4-,5-,6+,7-,8+/m1/s1
InChIKeyDYCCLPFFILCZGU-CBQIKETKSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC(=O)N[C@H]1[C@@H](O)S[C@H](CO)[C@H](O)[C@@H]1O
CACTVS 3.385CC(=O)N[CH]1[CH](O)S[CH](CO)[CH](O)[CH]1O
OpenEye OEToolkits 1.7.6CC(=O)NC1C(C(C(SC1O)CO)O)O
OpenEye OEToolkits 1.7.6CC(=O)N[C@@H]1[C@H]([C@H]([C@H](S[C@@H]1O)CO)O)O
ACDLabs 12.01C1(O)C(C(O)C(C(S1)CO)O)NC(C)=O
FormulaC8 H15 N O5 S
Name2-acetamido-2-deoxy-5-thio-alpha-D-galactopyranose;
2-(acetylamino)-2-deoxy-5-thio-alpha-D-galactopyranose;
2-acetamido-2-deoxy-5-thio-alpha-D-galactose;
2-acetamido-2-deoxy-5-thio-D-galactose;
2-acetamido-2-deoxy-5-thio-galactose
ChEMBL
DrugBank
ZINCZINC000098208695
PDB chain4d0z Chain E Residue 1584 [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]
PDB4d0z Substrate-Guided Front-Face Reaction Revealed by Combined Structural Snapshots and Metadynamics for the Polypeptide N- Acetylgalactosaminyltransferase 2.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		D458 L460 Y471 H474 N479
Binding residue
(residue number reindexed from 1)		D384 L386 Y397 H400 N405
Annotation score1
Enzymatic activity
Enzyme Commision number 2.4.1.41: polypeptide N-acetylgalactosaminyltransferase.
Gene Ontology
Molecular Function
GO:0004653 polypeptide N-acetylgalactosaminyltransferase activity
GO:0005515 protein binding
GO:0016757 glycosyltransferase activity
GO:0030145 manganese ion binding
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
GO:0018242 protein O-linked glycosylation via serine
GO:0018243 protein O-linked glycosylation via threonine
GO:0051604 protein maturation
Cellular Component
GO:0000139 Golgi membrane
GO:0005576 extracellular region
GO:0005789 endoplasmic reticulum membrane
GO:0005794 Golgi apparatus
GO:0005795 Golgi stack
GO:0016020 membrane
GO:0032580 Golgi cisterna membrane
GO:0048471 perinuclear region of cytoplasm

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4d0z, PDBe:4d0z, PDBj:4d0z
PDBsum4d0z
PubMed24954443
UniProtQ10471|GALT2_HUMAN Polypeptide N-acetylgalactosaminyltransferase 2 (Gene Name=GALNT2)

[Back to BioLiP]