Structure of PDB 2f2h Chain D Binding Site BS01

Receptor Information
>2f2h Chain D (length=773) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKISDGNWLIQPGLNLIHPLQVFEVEQQDNEMVVYAAPRDVRERTWQLDT
PLFTLRFFSPQEGIVGVRIEHFQGALNNGPHYPLNILQDVKVTIENTERY
AEFKSGNLSARVSKGEFWSLDFLRNGERITGSQVKNNGYVQDTNNQRNYM
FERLDLGVGETVYGLGERFTALVRNGQTVETWNRDGGTSTEQAYKNIPFY
MTNRGYGVLVNHPQCVSFEVGSEKVSKVQFSVESEYLEYFVIDGPTPKAV
LDRYTRFTGRPALPPAWSFGLWLTTSFTTNYDEATVNSFIDGMAERNLPL
HVFHFDCFWMKAFQWCDFEWDPLTFPDPEGMIRRLKAKGLKICVWINPYI
GQKSPVFKELQEKGYLLKRPDGSLWQWDKWQPGLAIYDFTNPDACKWYAD
KLKGLVAMGVDCFKTDFGERIPTDVQWFDGSDPQKMHNHYAYIYNELVWN
VLKDTVGEEEAVLFARSASVGAQKFPVHWGGDCYANYESMAESLRGGLSI
GLSGFGFWSHDIGGFENTAPAHVYKRWCAFGLLSSHSRLHGSKSYRVPWA
YDDESCDVVRFFTQLKCRMMPYLYREAARANARGTPMMRAMMMEFPDDPA
CDYLDRQYMLGDNVMVAPVFTEAGDVQFYLPEGRWTHLWHNDELDGSRWH
KQQHGFLSLPVYVRDNTLLALGNNDQRPDYVWHEGTAFHLFNLQDGHEAV
CEVPAADGSVIFTLKAARTGNTITVTGAGEAKNWTLCLRNVVKVNGLQDG
SQAESEQGLVVKPQGNALTITLH
Ligand information
Ligand IDXTG
InChIInChI=1S/C17H23NO11S/c19-9-5-27-17(15(24)11(9)20)30-6-10-12(21)13(22)14(23)16(29-10)28-8-3-1-7(2-4-8)18(25)26/h1-4,9-17,19-24H,5-6H2/t9-,10-,11+,12-,13+,14-,15-,16-,17-/m1/s1
InChIKeyHQYVHBCTLFPWRQ-ZMFOIVQCSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1cc(ccc1[N+](=O)[O-])O[C@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CS[C@@H]3[C@@H]([C@H]([C@@H](CO3)O)O)O)O)O)O
CACTVS 3.341O[C@@H]1CO[C@H](SC[C@H]2O[C@@H](Oc3ccc(cc3)[N+]([O-])=O)[C@H](O)[C@@H](O)[C@@H]2O)[C@H](O)[C@H]1O
CACTVS 3.341O[CH]1CO[CH](SC[CH]2O[CH](Oc3ccc(cc3)[N+]([O-])=O)[CH](O)[CH](O)[CH]2O)[CH](O)[CH]1O
OpenEye OEToolkits 1.5.0c1cc(ccc1[N+](=O)[O-])OC2C(C(C(C(O2)CSC3C(C(C(CO3)O)O)O)O)O)O
ACDLabs 10.04[O-][N+](=O)c3ccc(OC2OC(CSC1OCC(O)C(O)C1O)C(O)C(O)C2O)cc3
FormulaC17 H23 N O11 S
Name4-NITROPHENYL 6-THIO-6-S-ALPHA-D-XYLOPYRANOSYL-BETA-D-GLUCOPYRANOSIDE;
4-NITROPHENYL-(6-S-ALPHA-D-XYLOPYRANOSYL)-BETA-D-GLUCOPYRANOSIDE
ChEMBL
DrugBankDB04807
ZINCZINC000012504521
PDB chain2f2h Chain D Residue 3018 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB2f2h Expanding the Thioglycoligase Strategy to the Synthesis of alpha-linked Thioglycosides Allows Structural Investigation of the Parent Enzyme/Substrate Complex
Resolution1.95 Å
Binding residue
(original residue number in PDB)		D185 D306 C307 K414 D416 R466 W479 D482 F515 H540
Binding residue
(residue number reindexed from 1)		D185 D306 C307 K414 D416 R466 W479 D482 F515 H540
Annotation score1
Binding affinityMOAD: Ki=2uM
PDBbind-CN: -logKd/Ki=5.70,Ki=2uM
Enzymatic activity
Enzyme Commision number 3.2.1.177: alpha-D-xyloside xylohydrolase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds
GO:0016798 hydrolase activity, acting on glycosyl bonds
GO:0030246 carbohydrate binding
GO:0042802 identical protein binding
GO:0061634 alpha-D-xyloside xylohydrolase
GO:0080176 xyloglucan 1,6-alpha-xylosidase activity
Biological Process
GO:0005975 carbohydrate metabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:2f2h, PDBe:2f2h, PDBj:2f2h
PDBsum2f2h
PubMed16478160
UniProtP31434|XYLS_ECOLI Alpha-xylosidase (Gene Name=yicI)

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