Structure of PDB 2c59 Chain B Binding Site BS01

Receptor Information
>2c59 Chain B (length=362) Species: 3702 (Arabidopsis thaliana) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GAYTYKELEREQYWPSENLKISITGAGGFIASHIARRLKHEGHYVIASDW
KKNEHMTEDMFCDEFHLVDLRVMENCLKVTEGVDHVFNLAADMGGMGFIQ
SNHSVIMYNNTMISFNMIEAARINGIKRFFYASSACIYPEFKQLETTNVS
LKESDAWPAEPQDAYGLEKLATEELCKHYNKDFGIECRIGRFHNIYGPFG
TWKGGREKAPAAFCRKAQTSTDRFEMWGDGLQTRSFTFIDECVEGVLRLT
KSDFREPVNIGSDEMVSMNEMAEMVLSFEEKKLPIHHIPGPEGVRGRNSD
NNLIKEKLGWAPNMRLKEGLRITYFWIKEQIEKEKAKGSDVSLYGSSKVV
GTQAPVQLGSLR
Ligand information
Ligand IDGDD
InChIInChI=1S/C16H25N5O16P2/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/h3-5,7-11,14-15,22-27H,1-2H2,(H,29,30)(H,31,32)(H3,17,19,20,28)/t4-,5-,7-,8-,9+,10-,11+,14-,15-/m1/s1
InChIKeyMVMSCBBUIHUTGJ-GDJBGNAASA-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@@H](O)[C@H](O)[C@@H]4O)[C@@H](O)[C@H]3O
ACDLabs 10.04O=P(OC1OC(C(O)C(O)C1O)CO)(O)OP(=O)(O)OCC4OC(n2c3N=C(N)NC(=O)c3nc2)C(O)C4O
OpenEye OEToolkits 1.5.0c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OC4C(C(C(C(O4)CO)O)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@@H]([C@H](O4)CO)O)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)[CH](O)[CH](O)[CH]4O)[CH](O)[CH]3O
FormulaC16 H25 N5 O16 P2
NameGUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE
ChEMBL
DrugBank
ZINCZINC000008215581
PDB chain2c59 Chain B Residue 1377 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2c59 Structure and Function of Gdp-Mannose-3',5'-Epimerase: An Enzyme which Performs Three Chemical Reactions at the Same Active Site.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		G103 G104 M105 I108 S143 C145 Y174 F201 H202 N203 K217 A218 A221 F222 K225 W236 Q241 R243 M277 P300 E301 S356
Binding residue
(residue number reindexed from 1)		G94 G95 M96 I99 S134 C136 Y165 F192 H193 N194 K208 A209 A212 F213 K216 W227 Q232 R234 M268 P291 E292 S347
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) S143 A144 C145 Y174 K178 K217
Catalytic site (residue number reindexed from 1) S134 A135 C136 Y165 K169 K208
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
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Biological Process
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Cellular Component
External links
PDB RCSB:2c59, PDBe:2c59, PDBj:2c59
PDBsum2c59
PubMed16366586
UniProtQ93VR3|GME_ARATH GDP-mannose 3,5-epimerase (Gene Name=At5g28840)

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