Structure of PDB 2vl4 Chain A Binding Site BS01

Receptor Information
>2vl4 Chain A (length=836) Species: 226186 (Bacteroides thetaiotaomicron VPI-5482) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NDTSEVMLLDTGWEFSQSGTEKWMPATVPGTVHQDLISHELLPNPFYGMN
EKKIQWVENEDWEYRTSFIVSEEQLNRDGIQLIFEGLDTYADVYLNGSLL
LKADNMFVGYTLPVKSVLRKGENHLYIYFHSPIRQTLPQYASNGFNYPAD
NDHHEKHLSVFSRKAPYSYGWDWGIRMVTSGVWRPVTLRFYDIATISDYY
VRQLSLTDENARLSNELIVNQIVPQKIPAEVRVNVSLNGTTVTEVKQQVT
LQPGINHITLPAEVTNPVRWMPNGWGTPTLYDFSAQIACGDRIVAEQSHR
IGLRTIRVVNEKDKDGESFYFEVNGIPMFAKGANYIPQDALLPNVTTERY
QTLFRDMKEANMNMVRIWGGGTYENNLFYDLADENGILVWQDFMFACTPY
PSDPTFLKRVEAEAVYNIRRLRNHASLAMWCGNNEILEALKYWGFEKKFT
PEVYQGLMHGYDKLFRELLPSTVKEFDSDRFYVHSSPYLANWGRPESWGT
GDSHNWGVWYGKKPFESLDTDLPRFMSEFGFQSFPEMKTIAAFAAPEDYQ
IESEVMNAHQKSSIGNSLIRTYMERDYIIPESFEDFVYVGLVLQGQGMRH
GLEAHRRNRPYCMGTLYWQLNDSWPVVSWSSIDYYGNWKALHYQAKRAFA
PVLINPIQQNDSLSVYLISDRLDTMEQMTLEMKVVDFDGKTLGKKIQVHS
LEVPANTSKCVYRAKLDGWLTPEDCRRSFLKLILKDKSGHQVAESVHFFR
KTKDLQLPPTSVSYQMKQTDGKCELTLFSSMLAKDIFIETPLQGARYSDN
FFDLLPGERKKVIITSPRIKKEELPVNIKHIRETYK
Ligand information
Ligand IDMNM
InChIInChI=1S/C6H13NO4/c8-2-3-1-7-6(11)5(10)4(3)9/h3-11H,1-2H2/t3-,4-,5+,6+/m1/s1
InChIKeyBHOYFRIRWXBNHP-ZXXMMSQZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C1C(C(C(C(N1)O)O)O)CO
CACTVS 3.341OC[CH]1CN[CH](O)[CH](O)[CH]1O
CACTVS 3.341OC[C@H]1CN[C@@H](O)[C@@H](O)[C@@H]1O
OpenEye OEToolkits 1.5.0C1[C@@H]([C@H]([C@@H]([C@@H](N1)O)O)O)CO
ACDLabs 10.04OC1C(CNC(O)C1O)CO
FormulaC6 H13 N O4
Name(2S,3S,4R,5R)-2,3,4-TRIHYDROXY-5-HYDROXYMETHYL-PIPERIDINE
ChEMBL
DrugBank
ZINC
PDB chain2vl4 Chain A Residue 1865 [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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PDB2vl4 Structural and Biochemical Evidence for a Boat-Like Transition State in Beta-Mannosidases.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		W198 D199 W200 W395 N461 E462 W533 Y537 E555 W645 W656
Binding residue
(residue number reindexed from 1)		W171 D172 W173 W368 N434 E435 W506 Y510 E528 W618 W629
Annotation score1
Binding affinityMOAD: Ki=975nM
PDBbind-CN: -logKd/Ki=6.01,Ki=975nM
Enzymatic activity
Enzyme Commision number 3.2.1.25: beta-mannosidase.
Gene Ontology
Molecular Function
GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds
GO:0004567 beta-mannosidase activity
GO:0016798 hydrolase activity, acting on glycosyl bonds
Biological Process
GO:0005975 carbohydrate metabolic process
GO:0006516 glycoprotein catabolic process
Cellular Component
GO:0005576 extracellular region

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2vl4, PDBe:2vl4, PDBj:2vl4
PDBsum2vl4
PubMed18408714
UniProtQ8AAK6

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