Structure of PDB 6h0n Chain B Binding Site BS02

Receptor Information
>6h0n Chain B (length=370) Species: 3702 (Arabidopsis thaliana) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RVDLDGKPIQPLTICMIGAGGFIGSHLCEKLLTETPHKVLALDVYNDKIK
HLLERIQFHRINIKHDSRLEGLVKMADLIINLAAICTPADYNTRPLDTIY
SNFIDALPVVKYCSENNKRLIHFSTCEVYGKTIGSFLPKDHPLRDDPAFY
VLKEDISPCIFGSIEKQRWSYACAKQLIERLVYAEGAENGLEFTIVRPFN
WIGPRMDFIPGIDGPSEGVPRVLACFSNNLLRREPLKLVDGGESQRTFVY
INDAIEAVLLMIENPERANGHIFNVGNPNNEVTVRQLAEMMTEVYAKVSG
EGAIESPTVDVSSKEFYGEGYDDSDKRIPDMTIINRQLGWNPKTSLWDLL
ESTLTYQHRTYAEAVKKATS
Ligand information
Ligand IDUDP
InChIInChI=1S/C9H14N2O12P2/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(22-8)3-21-25(19,20)23-24(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
InChIKeyXCCTYIAWTASOJW-XVFCMESISA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)(O)OP(=O)(O)O)O)O
CACTVS 3.370O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
CACTVS 3.370O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
OpenEye OEToolkits 1.7.0C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)O)O)O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)C(O)C2O
FormulaC9 H14 N2 O12 P2
NameURIDINE-5'-DIPHOSPHATE
ChEMBLCHEMBL130266
DrugBankDB03435
ZINCZINC000004490939
PDB chain6h0n Chain B Residue 402 [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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PDB6h0n Deciphering the enzymatic mechanism of sugar ring contraction in UDP-apiose biosynthesis.
Resolution3.02 Å
Binding residue
(original residue number in PDB)		P102 R182 R235 V236 C239 K251 L252 V253 R260 V298 F330 Y331 Y335 D337 R341
Binding residue
(residue number reindexed from 1)		P88 R168 R221 V222 C225 K237 L238 V239 R246 V284 F316 Y317 Y321 D323 R327
Annotation score2
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0016831 carboxy-lyase activity
GO:0042802 identical protein binding
GO:0042803 protein homodimerization activity
GO:0046982 protein heterodimerization activity
GO:0048040 UDP-glucuronate decarboxylase activity
GO:0051287 NAD binding
GO:0102765 UDP-D-apiose synthase activity
Biological Process
GO:0009226 nucleotide-sugar biosynthetic process
GO:0010396 rhamnogalacturonan II metabolic process
GO:0033320 UDP-D-xylose biosynthetic process
GO:0033352 UDP-D-apiose biosynthetic process
GO:0071555 cell wall organization
Cellular Component
GO:0005737 cytoplasm
GO:0005777 peroxisome
GO:0005829 cytosol

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6h0n, PDBe:6h0n, PDBj:6h0n
PDBsum6h0n
PubMed31844840
UniProtQ9ZUY6|AXS1_ARATH UDP-D-apiose/UDP-D-xylose synthase 1 (Gene Name=AXS1)

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