Structure of PDB 4d11 Chain D Binding Site BS05

Receptor Information
>4d11 Chain D (length=487) 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
DMMMDVWGGENLEISFRVWQCGGSLEIIPCSRVGHVFRKQHPYTFARNTR
RAAEVWMDEYKNFYYAAVPSARNVPYGNIQSRLELRKKLSCKPFKWYLEN
VYPELRVPDHQDIAFGALQQGTNCLDTLGHFADGVVGVYECHNAGGNQEW
ALTKEKSVKHMDLCLTVVDRAPGSLIKLQGCREDDSRQKWEQIEGNSKLR
HVGSNLCLDSRTAKSGGLSVEVCGPALSQQWKFTLNL
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 chain4d11 Chain D Residue 1572 [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]
PDB4d11 Substrate-Guided Front-Face Reaction Revealed by Combined Structural Snapshots and Metadynamics for the Polypeptide N- Acetylgalactosaminyltransferase 2.
Resolution2.85 Å
Binding residue
(original residue number in PDB)		D458 H474 N479
Binding residue
(residue number reindexed from 1)		D376 H392 N397
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:4d11, PDBe:4d11, PDBj:4d11
PDBsum4d11
PubMed24954443
UniProtQ10471|GALT2_HUMAN Polypeptide N-acetylgalactosaminyltransferase 2 (Gene Name=GALNT2)

[Back to BioLiP]