Structure of PDB 2fyv Chain A Binding Site BS02

Receptor Information

>2fyv Chain A (length=1014) Species: 7227 (Drosophila melanogaster)

CQDVVQDVPNVDVQMLELYDRMSFKDIDGGVWKQGWNIKYDPLKYNAHHK
LKVFVVPHSHNDPGWIQTFEEYYQHDTKHILSNALRHLHDNPEMKFIWAE
ISYFARFYHDLGENKKLQMKSIVKNGQLEFVTGGWVMPDEANSHWRNVLL
QLTEGQTWLKQFMNVTPTASWAIDPFGHSPTMPYILQKSGFKNMLIQRTH
YSVKKELAQQRQLEFLWRQIWDNKGDTALFTHMMPFYSYDIPHTCGPDPK
VCCQFDFKRMGSFGLSCPWKVPPRTISDQNVAARSDLLVDQWKKKAELYR
TNVLLIPLGDDFRFKQNTEWDVQRVNYERLFEHINSQAHFNVQAQFGTLQ
EYFDAVHQAERAGQAEFPTLSGDFFTYADRSDNYWSGYYTSRPYHKRMDR
VLMHYVRAAEMLSAWHSWDGMARIEERLEQARRELSLFQHHDGITGTAKT
HVVVDYEQRMQEALKACQMVMQQSVYRLLTKPSIYSPDFSFSYFTLDDSR
WPGSGVEDSRTTIILGEDILPSKHVVMHNTLPHWREQLVDFYVSSPFVSV
TDLANNPVEAQVSPVWSWHHDTLTKTIHPQGSTTKYRIIFKARVPPMGLA
TYVLTISDSKPEHTSYASNLLLRKNPTSLPLGQYPEDVKFGDPREISLRV
GNGPTLAFSEQGLLKSIQLTQDSPHVPVHFKFLKYGVRSHGDRSGAYLFL
PNGPASPVELGQPVVLVTKGKLESSVSVGLPSVVHQTIMRGGAPEIRNLV
DIGSLDNTEIVMRLETHIDSGDIFYTDLNGLQFIKRRRLDKLPLQANYYP
IPSGMFIEDANTRLTLLTGQPLGGSSLASGELEIMQDRRLASDDERGLGQ
GVLDNKPVLHIYRLVLEKVNNCVRPSKLHPAGYLTSAAHKASQSLLDPLD
KFIFAENEWIGAQGQFGGDHPSAREDLDVSVMRRLTKSSAKTQRVGYVLH
RTNLMQCGTPEEHTQKLDVCHLLPNVARCERTTLTFLQNLEHLDGMVAPE
VCPMETAAYVSSHS

Ligand information

• Ligand ID: W72
• InChI: InChI=1S/C11H21NO9/c13-3-4-7(16)5(14)1-12(4)2-6(15)8(17)9(18)10(19)11(20)21/h4-10,13-19H,1-3H2,(H,20,21)/t4-,5-,6+,7-,8-,9+,10-/m1/s1
• InChIKey: ULVYPTHABPSARY-OMCDLXCCSA-N
• SMILES:
  CACTVS 3.341: OC[CH]1[CH](O)[CH](O)CN1C[CH](O)[CH](O)[CH](O)[CH](O)C(O)=O
  OpenEye OEToolkits 1.5.0: C1C(C(C(N1CC(C(C(C(C(=O)O)O)O)O)O)CO)O)O
  OpenEye OEToolkits 1.5.0: C1[C@H]([C@@H]([C@H]([N@@]1C[C@@H]([C@H]([C@@H]([C@H](C(=O)O)O)O)O)O)CO)O)O
  ACDLabs 10.04: O=C(O)C(O)C(O)C(O)C(O)CN1C(C(O)C(O)C1)CO
  CACTVS 3.341: OC[C@@H]1[C@@H](O)[C@H](O)CN1C[C@H](O)[C@@H](O)[C@H](O)[C@@H](O)C(O)=O
• Formula: C11 H21 N O9
• Name: 6-DEOXY-6-[(2R,3R,4R)-3,4-DIHYDROXY-2-(HYDROXYMETHYL)PYRROLIDIN-1-YL]-L-GULONIC ACID
• ZINC: ZINC000058649978
• PDB chain: 2fyv Chain A Residue 2000

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2fyv Synthesis, enzymatic activity, and X-ray crystallography of an unusual class of amino acids.
• Resolution: 1.9 Å
• Binding residue (original residue number in PDB): D92 W95 D204 F206 S268 Y269 D340 D341 H471 D472 Y727 R876
• Binding residue (residue number reindexed from 1): D62 W65 D174 F176 S238 Y239 D310 D311 H441 D442 Y697 R846
• Annotation score: 1
• Binding affinity: MOAD: ic50=0.3mM
  PDBbind-CN: -logKd/Ki=3.52,IC50=0.3mM

Enzymatic activity

• Catalytic site (original residue number in PDB): H90 D92 D204 D341 H471
• Catalytic site (residue number reindexed from 1): H60 D62 D174 D311 H441
• Enzyme Commision number: 3.2.1.114: mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase.

Gene Ontology

Molecular Function

• GO:0003824 catalytic activity
• GO:0004559 alpha-mannosidase activity
• GO:0004572 mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity
• GO:0015923 mannosidase activity
• GO:0016798 hydrolase activity, acting on glycosyl bonds
• GO:0030246 carbohydrate binding
• GO:0046872 metal ion binding

Biological Process

• GO:0005975 carbohydrate metabolic process
• GO:0006013 mannose metabolic process
• GO:0006486 protein glycosylation
• GO:0006491 N-glycan processing
• GO:0016063 rhodopsin biosynthetic process
• GO:0035010 encapsulation of foreign target

Cellular Component

• GO:0000139 Golgi membrane
• GO:0005783 endoplasmic reticulum
• GO:0005794 Golgi apparatus
• GO:0005795 Golgi stack
• GO:0016020 membrane

External links

• PDB: RCSB:2fyv, PDBe:2fyv, PDBj:2fyv
• PDBsum: 2fyv
• PubMed: 17010621
• UniProt: Q24451|MAN2_DROME Alpha-mannosidase 2 (Gene Name=alpha-Man-IIa)