Structure of PDB 2ri9 Chain A Binding Site BS02

Receptor Information
>2ri9 Chain A (length=475) Species: 5077 (Penicillium citrinum) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SNQAKADAVKEAFQHAWNGYMKYAFPHDELTPVSNGHADSRNGWGASAVD
ALSTAVIMGKADVVNAILEHVADIDFSKTSDTVSLFETTIRYLAGMLSGY
DLLQGPAKNLVDNQDLIDGLLDQSRNLADVLKFAFDTPSGVPYNNINITS
HGNDGATTNGLAVTGTLVLEWTRLSDLTGDEEYAKLSQKAESYLLKPQPS
SSEPFPGLVGSSININDGQFADSRVSWNGGDDSFYEYLIKMYVYDPKRFE
TYKDRWVLAAESTIKHLKSHPKSRPDLTFLSSYSNRNYDLSSQHLTCFDG
GSFLLGGTVLDRQDFIDFGLELVDGCEATYNSTLTKIGPDSWGWDPKKVP
SDQKEFYEKAGFYISSGSYVLRPEVIESFYYAHRVTGKEIYRDWVWNAFV
AINSTCRTDSGFAAVSDVNKANGGSKYDNQESFLFAEVMKYSYLAHSEDA
AWQVQKGGKNTFVYNTEAHPISVAR
Ligand information
Ligand IDLDY
InChIInChI=1S/C5H10O5/c6-2-1-10-5(9)4(8)3(2)7/h2-9H,1H2/t2-,3+,4+,5+/m1/s1
InChIKeySRBFZHDQGSBBOR-STGXQOJASA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C1C(C(C(C(O1)O)O)O)O
OpenEye OEToolkits 1.5.0C1[C@H]([C@@H]([C@@H]([C@H](O1)O)O)O)O
CACTVS 3.341O[CH]1CO[CH](O)[CH](O)[CH]1O
CACTVS 3.341O[C@@H]1CO[C@H](O)[C@@H](O)[C@H]1O
ACDLabs 10.04OC1C(O)COC(O)C1O
FormulaC5 H10 O5
Namealpha-D-lyxopyranose;
alpha-D-lyxose;
D-lyxose;
lyxose
ChEMBLCHEMBL1159661
DrugBank
ZINCZINC000003861573
PDB chain2ri9 Chain F Residue 2 [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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PDB2ri9 Modulation of activity by Arg407: structure of a fungal alpha-1,2-mannosidase in complex with a substrate analogue.
Resolution1.95 Å
Binding residue
(original residue number in PDB)		F1468 E1472 T1501 E1502
Binding residue
(residue number reindexed from 1)		F433 E437 T466 E467
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=3.22,Ki=0.6mM
Enzymatic activity
Catalytic site (original residue number in PDB) E1122 R1126 D1267 E1409
Catalytic site (residue number reindexed from 1) E87 R91 D232 E374
Enzyme Commision number 3.2.1.113: mannosyl-oligosaccharide 1,2-alpha-mannosidase.
Gene Ontology
Molecular Function
GO:0004571 mannosyl-oligosaccharide 1,2-alpha-mannosidase activity
GO:0005509 calcium ion binding
GO:0016798 hydrolase activity, acting on glycosyl bonds
GO:0046872 metal ion binding
Biological Process
GO:0005975 carbohydrate metabolic process
GO:0006486 protein glycosylation
GO:0036503 ERAD pathway
GO:1904382 mannose trimming involved in glycoprotein ERAD pathway
Cellular Component
GO:0005576 extracellular region
GO:0005783 endoplasmic reticulum
GO:0016020 membrane

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2ri9, PDBe:2ri9, PDBj:2ri9
PDBsum2ri9
PubMed18323617
UniProtP31723|MAN12_PENCI Mannosyl-oligosaccharide alpha-1,2-mannosidase (Gene Name=MSDC)

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