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Structure of PDB 2vo5 Chain A Binding Site BS01

Receptor Information

>2vo5 Chain A (length=833) Species: 226186 (Bacteroides thetaiotaomicron VPI-5482)

NDTSEVMLLDTGWEFSQSGTEKWMPATVPGTVHQDLISHELLPNPFYGMN
EKKIQWVENEDWEYRTSFIVSEEQLNRDGIQLIFEGLDTYADVYLNGSLL
LKADNMFVGYTLPVKSVLRKGENHLYIYFHSPIRQTLPQYASNGFNYPAD
NDHHEKHLSVFSRKAPYSYGWDWGIRMVTSGVWRPVTLRFYDIATISDYY
VRQLSLTDENARLSNELIVNQIVPQKIPAEVRVNVSLNGTTVTEVKQQVT
LQPGINHITLPAEVTNPVRWMPNGWGTPTLYDFSAQIACGDRIVAEQSHR
IGLRTIRVVNEKDKDGESFYFEVNGIPMFAKGANYIPQDALLPNVTTERY
QTLFRDMKEANMNMVRIWGGGTYENNLFYDLADENGILVWQDFMFACTPY
PSDPTFLKRVEAEAVYNIRRLRNHASLAMWCGNNEILEALKYWGFEKKFT
PEVYQGLMHGYDKLFRELLPSTVKEFDSDRFYVHSSPYLANWGRPESWGT
GDSHNWGVWYGKKPFESLDTDLPRFMSEFGFQSFPEMKTIAAFAAPEDYQ
IESEVMNAHQKSSIGNSLIRTYMERDYIIPESFEDFVYVGLVLQGQGMRH
GLEAHRRNRPYCMGTLYWQLNDSWPVVSWSSIDYYGNWKALHYQAKRAFA
PVLINPIQQNDSLSVYLISDRLDTMEQMTLEMKVVDFDGKTLGKKIQVHS
LEVPANTSKCVYRAKLDGWLTPEDCRRSFLKLILKDKSGHQVAESVHFFR
KTKDLQLPPTSVSYQMKQTDGKCELTLFSSMLAKDIFIETPLQGARYSDN
FFDLLPGERKKVIITSPRIKLPVNIKHIRETYK

Ligand information

• Ligand ID: VBZ
• InChI: InChI=1S/C15H21NO4/c17-8-11-6-12-13(18)14(19)15(11,20)9-16(12)7-10-4-2-1-3-5-10/h1-5,11-14,17-20H,6-9H2/t11-,12-,13-,14-,15-/m1/s1
• InChIKey: XOLGFLJPIWWVBX-KJWHEZOQSA-N
• SMILES:
  CACTVS 3.341: OC[C@H]1C[C@@H]2[C@@H](O)[C@@H](O)[C@@]1(O)CN2Cc3ccccc3
  ACDLabs 10.04: OCC2CC3N(Cc1ccccc1)CC2(O)C(O)C3O
  OpenEye OEToolkits 1.5.0: c1ccc(cc1)CN2CC3(C(CC2C(C3O)O)CO)O
  OpenEye OEToolkits 1.5.0: c1ccc(cc1)C[N@]2C[C@]3([C@H](C[C@@H]2[C@H]([C@H]3O)O)CO)O
  CACTVS 3.341: OC[CH]1C[CH]2[CH](O)[CH](O)[C]1(O)CN2Cc3ccccc3
• Formula: C15 H21 N O4
• Name: (1R,4R,5R,7R,8R)-2-Benzyl-5-hydroxymethyl-2-aza-bicyclo[2.2.2]octane-4,7,8-triol
• ZINC: ZINC000016052629
• PDB chain: 2vo5 Chain A Residue 1865

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2vo5 Structural and Biochemical Evidence for a Boat-Like Transition State in Beta-Mannosidases.
• Resolution: 2.3 Å
• Binding residue (original residue number in PDB): W198 D199 W200 W395 N461 E462 W470 W533 Y537 E555 W645 W656
• Binding residue (residue number reindexed from 1): W171 D172 W173 W368 N434 E435 W443 W506 Y510 E528 W618 W629
• Annotation score: 1
• Binding affinity: MOAD: Ki=13uM
  PDBbind-CN: -logKd/Ki=4.89,Ki=13uM
  BindingDB: Ki=1.3e+4nM

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

External links

• PDB: RCSB:2vo5, PDBe:2vo5, PDBj:2vo5
• PDBsum: 2vo5
• PubMed: 18408714
• UniProt: Q8AAK6

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