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Structure of PDB 2vl4 Chain B Binding Site BS01

Receptor Information >2vl4 Chain B (length=841) Species: 226186 (Bacteroides thetaiotaomicron VPI-5482) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure] GNDTSEVMLLDTGWEFSQSGTEKWMPATVPGTVHQDLISHELLPNPFYGM NEKKIQWVENEDWEYRTSFIVSEEQLNRDGIQLIFEGLDTYADVYLNGSL LLKADNMFVGYTLPVKSVLRKGENHLYIYFHSPIRQTLPQYASNGFNYPA DNDHHEKHLSVFSRKAPYSYGWDWGIRMVTSGVWRPVTLRFYDIATISDY YVRQLSLTDENARLSNELIVNQIVPQKIPAEVRVNVSLNGTTVTEVKQQV TLQPGINHITLPAEVTNPVRWMPNGWGTPTLYDFSAQIACGDRIVAEQSH RIGLRTIRVVNEKDKDGESFYFEVNGIPMFAKGANYIPQDALLPNVTTER YQTLFRDMKEANMNMVRIWGGGTYENNLFYDLADENGILVWQDFMFACTP YPSDPTFLKRVEAEAVYNIRRLRNHASLAMWCGNNEILEALKYWGFEKKF TPEVYQGLMHGYDKLFRELLPSTVKEFDSDRFYVHSSPYLANWGRPESWG TGDSHNWGVWYGKKPFESLDTDLPRFMSEFGFQSFPEMKTIAAFAAPEDY QIESEVMNAHQKSSIGNSLIRTYMERDYIIPESFEDFVYVGLVLQGQGMR HGLEAHRRNRPYCMGTLYWQLNDSWPVVSWSSIDYYGNWKALHYQAKRAF APVLINPIQQNDSLSVYLISDRLDTMEQMTLEMKVVDFDGKTLGKKIQVH SLEVPANTSKCVYRAKLDGWLTPEDCRRSFLKLILKDKSGHQVAESVHFF RKTKDLQLPPTSVSYQMKQTDGKCELTLFSSMLAKDIFIETPLQGARYSD NFFDLLPGERKKVIITSPRIKKGEELPVNIKHIRETYKEHH

Ligand information Ligand ID MNM InChI InChI=1S/C6H13NO4/c8-2-3-1-7-6(11)5(10)4(3)9/h3-11H,1-2H2/t3-,4-,5+,6+/m1/s1 InChIKey BHOYFRIRWXBNHP-ZXXMMSQZSA-N SMILES Software SMILES OpenEye OEToolkits 1.5.0 C1C(C(C(C(N1)O)O)O)CO CACTVS 3.341 OC[CH]1CN[CH](O)[CH](O)[CH]1O CACTVS 3.341 OC[C@H]1CN[C@@H](O)[C@@H](O)[C@@H]1O OpenEye OEToolkits 1.5.0 C1[C@@H]([C@H]([C@@H]([C@@H](N1)O)O)O)CO ACDLabs 10.04 OC1C(CNC(O)C1O)CO Formula C6 H13 N O4 Name (2S,3S,4R,5R)-2,3,4-TRIHYDROXY-5-HYDROXYMETHYL-PIPERIDINE ChEMBL DrugBank ZINC PDB chain 2vl4 Chain B Residue 1868 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure Global view Local view Structure summary [Spin on] [Spin off] [Reset] [High quality] [Low quality] [White background] [Black background] [Spin on] [Spin off] [Reset] [High quality] [Low quality] [White background] [Black background] PDB 2vl4 Structural and Biochemical Evidence for a Boat-Like Transition State in Beta-Mannosidases. Resolution 1.9 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) W172 D173 W174 W369 N435 E436 W507 Y511 E529 W619 W630 Annotation score 1 Binding affinity MOAD: 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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