Structure of PDB 3a6o Chain B Binding Site BS02

Receptor Information
>3a6o Chain B (length=585) Species: 2026 (Thermoactinomyces vulgaris) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MLLEAIFHEAKGSYAYPISETQLRVRLRAKKGDVVRCEVLYADRYASPEE
ELAHALAGKAGSDERFDYFEALLECSTKRVKYVFLLTGPQGEAVYFGETG
FSAERSKAGVFQYAYIHRSEVFTTPEWAKEAVIYQIFPERFANGDPSNDP
PGTEQWAKDARPRHDSFYGGDLKGVIDRLPYLEELGVTALYFTPIFASPS
HHKYDTADYLAIDPQFGDLPTFRRLVDEAHRRGIKIILDAVFNHAGDQFF
AFRDVLQKGEQSRYKDWFFIEDFPVSKTSRTNYETFAVQVPAMPKLRTEN
PEVKEYLFDVARFWMEQGIDGWRLDVANEVDHAFWREFRRLVKSLNPDAL
IVGEIWHDASGWLMGDQFDSVMNYLFRESVIRFFATGEIHAERFDAELTR
ARMLYPEQAAQGLWNLLDSHDTERFLTSCGGNEAKFRLAVLFQMTYLGTP
LIYYGDEIGMAGATDPDCRRPMIWEEKEQNRGLFEFYKELIRLRHRLASL
TRGNVRSWHADKQANLYAFVRTVQDQHVGVVLNNRGEKQTVLLQVPESGG
KTWLDCLTGEEVHGKQGQLKLTLRPYQGMILWNGR
Ligand information
Ligand IDARE
InChIInChI=1S/C31H53NO23/c1-7-13(16(39)22(45)29(49-7)54-26-11(5-35)50-28(48)21(44)19(26)42)32-9-2-8(3-33)25(18(41)14(9)37)53-31-24(47)20(43)27(12(6-36)52-31)55-30-23(46)17(40)15(38)10(4-34)51-30/h2,7,9-48H,3-6H2,1H3/t7-,9+,10-,11-,12-,13-,14+,15-,16+,17+,18-,19-,20-,21-,22-,23-,24-,25-,26-,27-,28+,29-,30-,31-/m1/s1
InChIKeyJUCZMZWYUIRMPL-NPPSNIQKSA-N
SMILES
SoftwareSMILES
CACTVS 3.341C[CH]1O[CH](O[CH]2[CH](O)[CH](O)[CH](O)O[CH]2CO)[CH](O)[CH](O)[CH]1N[CH]3C=C(CO)[CH](O[CH]4O[CH](CO)[CH](O[CH]5O[CH](CO)[CH](O)[CH](O)[CH]5O)[CH](O)[CH]4O)[CH](O)[CH]3O
OpenEye OEToolkits 1.5.0CC1C(C(C(C(O1)OC2C(OC(C(C2O)O)O)CO)O)O)NC3C=C(C(C(C3O)O)OC4C(C(C(C(O4)CO)OC5C(C(C(C(O5)CO)O)O)O)O)O)CO
OpenEye OEToolkits 1.5.0C[C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O[C@@H]2[C@H](O[C@@H]([C@@H]([C@H]2O)O)O)CO)O)O)N[C@H]3C=C([C@H]([C@@H]([C@H]3O)O)O[C@@H]4[C@@H]([C@H]([C@@H]([C@H](O4)CO)O[C@@H]5[C@@H]([C@H]([C@@H]([C@H](O5)CO)O)O)O)O)O)CO
CACTVS 3.341C[C@H]1O[C@H](O[C@H]2[C@H](O)[C@@H](O)[C@@H](O)O[C@@H]2CO)[C@H](O)[C@@H](O)[C@@H]1N[C@H]3C=C(CO)[C@@H](O[C@H]4O[C@H](CO)[C@@H](O[C@H]5O[C@H](CO)[C@@H](O)[C@H](O)[C@H]5O)[C@H](O)[C@H]4O)[C@H](O)[C@H]3O
ACDLabs 10.04O(C3C(=CC(NC2C(OC(OC1C(O)C(O)C(O)OC1CO)C(O)C2O)C)C(O)C3O)CO)C5OC(C(OC4OC(CO)C(O)C(O)C4O)C(O)C5O)CO
FormulaC31 H53 N O23
NameACARBOSE DERIVED PENTASACCHARIDE;
4-O-(4,6-DIDEOXY-4-{[4-[(4-O-HEXOPYRANOSYLHEXOPYRANOSYL)OXY]-5,6-DIHYDROXY-3-(HYDROXYMETHYL)CYCLOHEX-2-EN-1-YL]AMINO}HE XOPYRANOSYL)HEXOPYRANOSE
ChEMBL
DrugBankDB04453
ZINCZINC000263620623
PDB chain3a6o Chain B Residue 702 [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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PDB3a6o Complex structures of Thermoactinomyces vulgaris R-47 alpha-amylase 2 with acarbose and cyclodextrins demonstrate the multiple substrate recognition mechanism
Resolution2.8 Å
Binding residue
(original residue number in PDB)		H164 H202 Y204 H244 F286 M293 R323 D325 E354 H420 D421 D465 R469
Binding residue
(residue number reindexed from 1)		H164 H202 Y204 H244 F286 M293 R323 D325 E354 H420 D421 D465 R469
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) D239 R323 D325 E354 H420 D421
Catalytic site (residue number reindexed from 1) D239 R323 D325 E354 H420 D421
Enzyme Commision number 3.2.1.135: neopullulanase.
Gene Ontology
Molecular Function
GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds
GO:0016798 hydrolase activity, acting on glycosyl bonds
GO:0031216 neopullulanase activity
GO:0046872 metal ion binding
Biological Process
GO:0005975 carbohydrate metabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3a6o, PDBe:3a6o, PDBj:3a6o
PDBsum3a6o
PubMed15138257
UniProtQ08751|NEPU2_THEVU Neopullulanase 2 (Gene Name=tvaII)

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