Structure of PDB 4bq3 Chain C Binding Site BS01

Receptor Information
>4bq3 Chain C (length=740) Species: 203122 (Saccharophagus degradans 2-40) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SHMLFDFENDQVPSNIHFLNARASIETYTGINGEPSKGLKLAMQSKQHSY
TGLAIVPEQPWDWSEFTSASLYFDIVSVGDHSTQFYLDVTDQNGAVFTRS
IDIPVGKMQSYYAKLSGHDLEVDLNLASGLRSNPPTWTSDDRQFVWMWGV
KNLDLSGIAKISLSVQSAMHDKTVIIDNIRIQPNPPQDENFLVGLVDEFG
QNAKVDYKGKIHSLEELHAARDVELAELDGKPMPSRSKFGGWLAGPKLKA
TGYFRTEKINGKWMLVDPEGYPYFATGLDIIRLSNSSTMTGYDYDQATVA
QRSADDVTPEDSKGLMAVSEKSFATRHLASPTRAAMFNWLPDYDHPLANH
YNYRRSAHSGPLKRGEAYSFYSANLERKYGETYPGSYLDKWREVTVDRML
NWGFTSLGNWTDPAYYDNNRIPFFANGWVIGDFKTVSSGADFWGAMPDVF
DPEFKVRAMETARVVSEEIKNSPWCVGVFIDNEKSFGRPDSDKAQYGIPI
HTLGRPSEGVPTRQAFSKLLKAKYKTIAALNNAWGLKLSSWAEFDLGVDV
KALPVTDTLRADYSMLLSAYADQYFKVVHGAVEHYMPNHLYLGARFPDWG
MPMEVVKAAAKYADVVSYNSYKEGLPKQKWAFLAELDKPSIIGEFHIGAM
DHGSYHPGLIHAASQADRGEMYKDYMQSVIDNPYFVGAHWFQYMDSPLTG
RAYDGENYNVGFVDVTDTPYQEMVDAAKEVNAKIYTERLG
Ligand information
Ligand ID47N
InChIInChI=1S/C12H20O10/c13-1-3-5(14)10(7(16)11(18)20-3)22-12-8(17)9-6(15)4(21-12)2-19-9/h3-18H,1-2H2/t3-,4+,5+,6-,7-,8+,9-,10+,11-,12+/m1/s1
InChIKeyJWMBOBQNPBCYER-AHBMTURSSA-N
SMILES
SoftwareSMILES
CACTVS 3.385OC[CH]1O[CH](O)[CH](O)[CH](O[CH]2O[CH]3CO[CH]([CH]3O)[CH]2O)[CH]1O
CACTVS 3.385OC[C@H]1O[C@@H](O)[C@H](O)[C@@H](O[C@@H]2O[C@H]3CO[C@H]([C@@H]3O)[C@@H]2O)[C@H]1O
ACDLabs 12.01O(C2OC1C(O)C(OC1)C2O)C3C(O)C(OC(O)C3O)CO
OpenEye OEToolkits 1.9.2C1C2C(C(O1)C(C(O2)OC3C(C(OC(C3O)O)CO)O)O)O
OpenEye OEToolkits 1.9.2C1[C@H]2[C@H]([C@@H](O1)[C@@H]([C@@H](O2)O[C@H]3[C@H]([C@H](O[C@H]([C@@H]3O)O)CO)O)O)O
FormulaC12 H20 O10
NameNEOAGAROBIOSE
ChEMBL
DrugBank
ZINCZINC000095635529
PDB chain4bq3 Chain C Residue 1792 [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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PDB4bq3 Substrate Recognition and Hydrolysis by a Family 50 Exo-Beta-Agarase Aga50D from the Marine Bacterium Saccharophagus Degradans
Resolution2.1 Å
Binding residue
(original residue number in PDB)		W199 F493 E534 R539 W650 L710
Binding residue
(residue number reindexed from 1)		W148 F442 E483 R488 W599 L659
Annotation score1
Enzymatic activity
Enzyme Commision number 3.2.1.81: beta-agarase.
Gene Ontology
Molecular Function
GO:0004565 beta-galactosidase activity
GO:0016798 hydrolase activity, acting on glycosyl bonds
GO:0033916 beta-agarase activity
GO:0046872 metal ion binding
Biological Process
GO:0005975 carbohydrate metabolic process
Cellular Component
GO:0009341 beta-galactosidase complex
GO:0016020 membrane

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Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4bq3, PDBe:4bq3, PDBj:4bq3
PDBsum4bq3
PubMed23921382
UniProtQ21HC5

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