Structure of PDB 5ndx Chain A Binding Site BS02

Receptor Information
>5ndx Chain A (length=606) Species: 386 (Rhizobium leguminosarum bv. trifolii) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MRERTRINVDASEAVRPFNRFWRGTGFSPAELLLEPEMRQMLAYIGGLPN
EGIKFLRVHYLYNLLSAKGGAGYDWSLLDRALDVMIEHRLKPFFELMGNP
SGLFTDYEDMDQVRRWRDLVTATVDRYGARYGMDELRTWYFETTNQADSG
WWTYGIKGYTNYYDACVAGLDAIDPSLPMGGPGTARTLSPIFRALMAHCD
SGTSCLTGDGPPRIDYISIHEKGVNGSKEDLTPKTNAIVDRTLLVVDYLK
EHHPRLAGLPIVNDECDPQLGWSDHHSWHGKAYYAGIIARIIEQHDRRII
APKAANFTFLSSDHAFIGGWSQRTIFAYFGSRNFTDVDRTPPFDIIKKPG
LTSMELLATLGDTVCKVTAEPPLDPDQDGLAILPTRLPGGGVSISLIHSV
DAINRSGRTAVRLEVSGLVPGRHAICLLRIDEEFTNPMEVWEAQRDESNP
RGPFEPVGAPPAPTEAQFAELRRAQEPALLHPISVVACDEGRISVDLDVP
LPSLTQVLVVPDVGVPPAAPTGLVVERYLGLGGREERMLFWAAGDISPAI
FYDVLVSTDGGTFEKVSSAPLISTAFLHMSPPEGVRYAVCARDAFGRRSE
LCLSRS
Ligand information
Ligand ID8U8
InChIInChI=1S/C16H16O9/c1-6-4-10(17)24-9-5-7(2-3-8(6)9)23-16-13(20)11(18)12(19)14(25-16)15(21)22/h2-5,11-14,16,18-20H,1H3,(H,21,22)/t11-,12-,13+,14+,16+/m0/s1
InChIKeyARQXEQLMMNGFDU-ZHMBSYLPSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6CC1=CC(=O)Oc2c1ccc(c2)O[C@H]3[C@@H]([C@H]([C@@H]([C@@H](O3)C(=O)O)O)O)O
CACTVS 3.385CC1=CC(=O)Oc2cc(O[C@@H]3O[C@H]([C@@H](O)[C@H](O)[C@H]3O)C(O)=O)ccc12
OpenEye OEToolkits 2.0.6CC1=CC(=O)Oc2c1ccc(c2)OC3C(C(C(C(O3)C(=O)O)O)O)O
CACTVS 3.385CC1=CC(=O)Oc2cc(O[CH]3O[CH]([CH](O)[CH](O)[CH]3O)C(O)=O)ccc12
FormulaC16 H16 O9
Name(2~{R},3~{S},4~{S},5~{R},6~{S})-6-(4-methyl-2-oxidanylidene-chromen-7-yl)oxy-3,4,5-tris(oxidanyl)oxane-2-carboxylic acid
ChEMBL
DrugBank
ZINCZINC000005724670
PDB chain5ndx Chain A Residue 713 [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]
PDB5ndx The bacterial orthologue of Human a-L-iduronidase does not need N-glycan post-translational modifications to be catalytically competent: Crystallography and QM/MM insights into Mucopolysaccharidosis I.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		K54 F55 F93 Y140 Y216 P260 V262 T308 F309
Binding residue
(residue number reindexed from 1)		K54 F55 F93 Y140 Y216 P260 V262 T308 F309
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds
GO:0016798 hydrolase activity, acting on glycosyl bonds
Biological Process
GO:0005975 carbohydrate metabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5ndx, PDBe:5ndx, PDBj:5ndx
PDBsum5ndx
PubMed
UniProtA0A1B8R7L2

[Back to BioLiP]