Structure of PDB 2c54 Chain B Binding Site BS02

Receptor Information
>2c54 Chain B (length=360) Species: 3702 (Arabidopsis thaliana) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
YTYKELEREQYWPSENLKISITGAGGFIASHIARRLKHEGHYVIASDWKK
NEHMTEDMFCDEFHLVDLRVMENCLKVTEGVDHVFNLAADMGGMGFIQSN
HSVIMYNNTMISFNMIEAARINGIKRFFYASSACIYPEFKQLETTNVSLK
ESDAWPAEPQDAYGLERLATEELCKHYNKDFGIECRIGRFHNIYGPFGTW
KGGREKAPAAFCRKAQTSTDRFEMWGDGLQTRSFTFIDECVEGVLRLTKS
DFREPVNIGSDEMVSMNEMAEMVLSFEEKKLPIHHIPGPEGVRGRNSDNN
LIKEKLGWAPNMRLKEGLRITYFWIKEQIEKEKAKGSDVSLYGSSKVVGT
QAPVQLGSLR
Ligand information
Ligand IDGKD
InChIInChI=1S/C16H23N5O16P2/c17-16-19-12-6(13(28)20-16)18-3-21(12)14-10(26)8(24)5(34-14)2-33-38(29,30)37-39(31,32)36-15-11(27)9(25)7(23)4(1-22)35-15/h3-5,8-11,14-15,22,24-27H,1-2H2,(H,29,30)(H,31,32)(H3,17,19,20,28)/t4-,5+,8+,9-,10+,11-,14+,15+/m0/s1
InChIKeyQZZKIVADHWVJFF-UFFCYROPSA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@](O)(=O)O[C@H]4O[C@@H](CO)C(=O)[C@H](O)[C@@H]4O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OC4C(C(C(=O)C(O4)CO)O)O)O)O)N=C(NC2=O)N
OpenEye OEToolkits 1.5.0c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@@](=O)(O)O[C@@H]4[C@H]([C@H](C(=O)[C@@H](O4)CO)O)O)O)O)N=C(NC2=O)N
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[CH]4O[CH](CO)C(=O)[CH](O)[CH]4O)[CH](O)[CH]3O
ACDLabs 10.04O=C1C(O)C(O)C(OC1CO)OP(=O)(O)OP(=O)(O)OCC4OC(n3cnc2c3N=C(N)NC2=O)C(O)C4O
FormulaC16 H23 N5 O16 P2
NameGUANOSINE 5'-DIPHOSPHATE-4-KETO-BETA-L-GULOSE
ChEMBL
DrugBank
ZINCZINC000058631614
PDB chain2c54 Chain B Residue 1374 [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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PDB2c54 Structure and function of GDP-mannose-3',5'-epimerase: an enzyme which performs three chemical reactions at the same active site.
Resolution1.5 Å
Binding residue
(original residue number in PDB)		G103 G104 M105 S143 F201 H202 N203 K217 A218 A221 F222 K225 W236 Q241 R243 M277 P300 E301 S356
Binding residue
(residue number reindexed from 1)		G92 G93 M94 S132 F190 H191 N192 K206 A207 A210 F211 K214 W225 Q230 R232 M266 P289 E290 S345
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) S143 A144 C145 Y174 R178 K217
Catalytic site (residue number reindexed from 1) S132 A133 C134 Y163 R167 K206
Enzyme Commision number 5.1.3.18: GDP-mannose 3,5-epimerase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0016853 isomerase activity
GO:0047918 GDP-mannose 3,5-epimerase activity
GO:0051287 NAD binding
Biological Process
GO:0019853 L-ascorbic acid biosynthetic process
Cellular Component
GO:0005829 cytosol
GO:0009536 plastid

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:2c54, PDBe:2c54, PDBj:2c54
PDBsum2c54
PubMed16366586
UniProtQ93VR3|GME_ARATH GDP-mannose 3,5-epimerase (Gene Name=At5g28840)

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