Structure of PDB 6gwf Chain A Binding Site BS01

Receptor Information
>6gwf Chain A (length=535) Species: 243274 (Thermotoga maritima MSB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LVPRGSHMASMEIFGKTFREGRFVLKEKNFTVEFAVEKIHLGWKISGRVK
GSPGRLEVLRTKAPEKVLVNNWQSWGPCRVVDAFSFKPPEIDPNWRYTAS
VVPDVLERNLQSDYFVAEEGKVYGFLSSKIAHPFFAVEDGELVAYLEYFD
VEFDDFVPLEPLVVLEDPNTPLLLEKYAELVGMENNARVPKHTPTGWCSW
YHYFLDLTWEETLKNLKLAKNFPFEVFQIDDAYEKDIGDWLVTRGDFPSV
EEMAKVIAENGFIPGIWTAPFSVSETSDVFNEHPDWVVKENGEPKMAYRN
WNKKIYALDLSKDEVLNWLFDLFSSLRKMGYRYFKIDFLFAGAVPGERKK
NITPIQAFRKGIETIRKAVGEDSFILGCGSPLLPAVGCVDGMRIGPATAP
FWGEHIEDNGAPAARWALRNAITRYFMHDRFWLNDPDCLILREEKTDLTQ
KEKELYSYTCGVLDNMIIESDDLSLVRDHGKKVLKETLELLGGRPRVQNI
MSEDLRYEIVSSGTLSGNVKIVVDLNSREYHLEKE
Ligand information
Ligand IDFEQ
InChIInChI=1S/C13H13FN2O8/c14-11-10(3-6(5-17)12(18)13(11)19)24-9-2-1-7(15(20)21)4-8(9)16(22)23/h1-4,10-13,17-19H,5H2/t10-,11-,12-,13+/m0/s1
InChIKeyWVAYSDIDYBKDLD-ZDEQEGDKSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6c1cc(c(cc1[N+](=O)[O-])[N+](=O)[O-])OC2C=C(C(C(C2F)O)O)CO
CACTVS 3.385OCC1=C[C@H](Oc2ccc(cc2[N+]([O-])=O)[N+]([O-])=O)[C@H](F)[C@@H](O)[C@H]1O
CACTVS 3.385OCC1=C[CH](Oc2ccc(cc2[N+]([O-])=O)[N+]([O-])=O)[CH](F)[CH](O)[CH]1O
OpenEye OEToolkits 2.0.6c1cc(c(cc1[N+](=O)[O-])[N+](=O)[O-])O[C@H]2C=C([C@@H]([C@@H]([C@H]2F)O)O)CO
FormulaC13 H13 F N2 O8
Name(1~{S},2~{S},5~{S},6~{R})-5-(2,4-dinitrophenoxy)-6-fluoranyl-3-(hydroxymethyl)cyclohex-3-ene-1,2-diol
ChEMBL
DrugBank
ZINC
PDB chain6gwf Chain A Residue 603 [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]
PDB6gwf Revealing the mechanism for covalent inhibition of glycoside hydrolases by carbasugars at an atomic level.
Resolution1.72 Å
Binding residue
(original residue number in PDB)
W65 W190 Y191 D220 D221 W257 K325 D327 F328 C368 R383
Binding residue
(residue number reindexed from 1)
W75 W200 Y201 D230 D231 W267 K335 D337 F338 C378 R393
Annotation score1
Enzymatic activity
Enzyme Commision number 3.2.1.22: alpha-galactosidase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0004557 alpha-galactosidase activity
GO:0016798 hydrolase activity, acting on glycosyl bonds
GO:0030246 carbohydrate binding
GO:0042803 protein homodimerization activity
Biological Process
GO:0005975 carbohydrate metabolic process
GO:0016139 glycoside catabolic process

View graph for
Molecular Function

View graph for
Biological Process
External links
PDB RCSB:6gwf, PDBe:6gwf, PDBj:6gwf
PDBsum6gwf
PubMed30104598
UniProtG4FEF4|AGAL_THEMA Alpha-galactosidase (Gene Name=galA)

[Back to BioLiP]