Structure of PDB 5m5d Chain A Binding Site BS01

Receptor Information
>5m5d Chain A (length=347) Species: 657309 (Bacteroides xylanisolvens XB1A) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LGTELDYDTFCFYYDWYGSEAIDGQYRHWAHAIAPDPNGGSGQNPGTIPG
TQESIASNFYPQLGRYSSSDPNILTKHMDMFVMARTGVLALTWWNEQDET
EAKRIGLILDAADKKKIKVCFHLEPYPSRNVQNLRENIVKLITRYGNHPA
FYRKDGKPLFFIYDSYLIEPSEWEKLLSPGGSITIRNTAYDALMIGLWTS
SPTVQRPFILNAHFDGFYTYFAATGFTYGSTPTNWVSMQKWAKENGKIFI
PSVGPGYIDTRIRPWNGSVIRTRTDGQYYDAMYRKAIEAGVSAISITSFN
EWHEGSQIEPAVPYTSSEFTYLDYENREPDYYLTRTAYWVGKFRESK
Ligand information
Ligand IDDGO
InChIInChI=1S/C6H10O4/c7-3-5-6(9)4(8)1-2-10-5/h1-2,4-9H,3H2/t4-,5-,6+/m1/s1
InChIKeyYVECGMZCTULTIS-PBXRRBTRSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01C=1OC(C(C(C=1)O)O)CO
CACTVS 3.385OC[CH]1OC=C[CH](O)[CH]1O
OpenEye OEToolkits 2.0.4C1=COC(C(C1O)O)CO
CACTVS 3.385OC[C@H]1OC=C[C@@H](O)[C@@H]1O
OpenEye OEToolkits 2.0.4C1=CO[C@@H]([C@H]([C@@H]1O)O)CO
FormulaC6 H10 O4
NameD-glucal
ChEMBLCHEMBL2115567
DrugBank
ZINCZINC000004284522
PDB chain5m5d 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

[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]
PDB5m5d Contribution of Shape and Charge to the Inhibition of a Family GH99 endo-alpha-1,2-Mannanase.
Resolution1.07 Å
Binding residue
(original residue number in PDB)		Y46 W126 H154 E156 Y195 Y252 E333 E336
Binding residue
(residue number reindexed from 1)		Y14 W94 H122 E124 Y163 Y220 E301 E304
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=3.95,Kd=111uM
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
View graph for
Cellular Component
External links
PDB RCSB:5m5d, PDBe:5m5d, PDBj:5m5d
PDBsum5m5d
PubMed27992199
UniProtD6D1V7

[Back to BioLiP]