Structure of PDB 5m17 Chain A Binding Site BS01

Receptor Information
>5m17 Chain A (length=349) Species: 657309 (Bacteroides xylanisolvens XB1A) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NNLGTELDYDTFCFYYDWYGSEAIDGQYRHWAHAIAPDPNGGSGQNPGTI
PGTQESIASNFYPQLGRYSSSDPNILTKHMDMFVMARTGVLALTWWNEQD
ETEAKRIGLILDAADKKKIKVCFHLEPYPSRNVQNLRENIVKLITRYGNH
PAFYRKDGKPLFFIYDSYLIEPSEWEKLLSPGGSITIRNTAYDALMIGLW
TSSPTVQRPFILNAHFDGFYTYFAATGFTYGSTPTNWVSMQKWAKENGKI
FIPSVGPGYIDTRIRPWNGSVIRTRTDGQYYDAMYRKAIEAGVSAISITS
FNEWHEGSQIEPAVPYTSSEFTYLDYENREPDYYLTRTAYWVGKFRESK
Ligand information
Ligand ID7D1
InChIInChI=1S/C6H12O4/c7-3-5-6(9)4(8)1-2-10-5/h4-9H,1-3H2/t4-,5-,6+/m1/s1
InChIKeyQFHKFGOUFKUPNX-PBXRRBTRSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6C1CO[C@@H]([C@H]([C@@H]1O)O)CO
CACTVS 3.385OC[C@H]1OCC[C@@H](O)[C@@H]1O
CACTVS 3.385OC[CH]1OCC[CH](O)[CH]1O
OpenEye OEToolkits 2.0.6C1COC(C(C1O)O)CO
FormulaC6 H12 O4
Name1,5-anhydro-2-deoxy-D-arabino-hexitol;
(2~{R},3~{S},4~{R})-2-(hydroxymethyl)oxane-3,4-diol;
1,2-dideoxy-D-mannopyranose
ChEMBL
DrugBank
ZINC
PDB chain5m17 Chain B Residue 1 [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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PDB5m17 Contribution of Shape and Charge to the Inhibition of a Family GH99 endo-alpha-1,2-Mannanase.
Resolution1.03 Å
Binding residue
(original residue number in PDB)		Y46 W126 H154 E156 Y195 Y252 E336
Binding residue
(residue number reindexed from 1)		Y16 W96 H124 E126 Y165 Y222 E306
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=3.66,Kd=221uM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0004559 alpha-mannosidase activity
GO:0016787 hydrolase activity
GO:0016798 hydrolase activity, acting on glycosyl bonds
Cellular Component
GO:0016020 membrane

View graph for
Molecular Function
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Cellular Component
External links
PDB RCSB:5m17, PDBe:5m17, PDBj:5m17
PDBsum5m17
PubMed27992199
UniProtD6D1V7

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