Structure of PDB 6h0p Chain A Binding Site BS02

Receptor Information
>6h0p Chain A (length=375) Species: 3702 (Arabidopsis thaliana) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VDLDGKPIQPLTICMIGAGGFIGSHLCEKLLTETPHKVLALDVYNDKIKH
LLEPDTVEWSGRIQFHRINIKHDSRLEGLVKMADLIINLAAIATPADYNT
RPLDTIYSNFIDALPVVKYCSENNKRLIHFSTCEVYGKTIGSFLPKDHPL
RDDPAFYVLKEDISPCIFGSIEKQRWSYACAKQLIERLVYAEGAENGLEF
TIVRPFNWIGPRMDFIPGIDGPSEGVPRVLACFSNNLLRREPLKLVDGGE
SQRTFVYINDAIEAVLLMIENPERANGHIFNVGNPNNEVTVRQLAEMMTE
VYAKVSGEGAIESPTVDVSSKEFYGEGYDDSDKRIPDMTIINRQLGWNPK
TSLWDLLESTLTYQHRTYAEAVKKA
Ligand information
Ligand IDUGA
InChIInChI=1S/C15H22N2O18P2/c18-5-1-2-17(15(26)16-5)12-9(22)6(19)4(32-12)3-31-36(27,28)35-37(29,30)34-14-10(23)7(20)8(21)11(33-14)13(24)25/h1-2,4,6-12,14,19-23H,3H2,(H,24,25)(H,27,28)(H,29,30)(H,16,18,26)/t4-,6-,7+,8+,9-,10-,11+,12-,14-/m1/s1
InChIKeyHDYANYHVCAPMJV-LXQIFKJMSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C(O)C3OC(OP(=O)(O)OP(=O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)C(O)C2O)C(O)C(O)C3O
CACTVS 3.341O[CH]1[CH](O)[CH](O[CH]([CH]1O)C(O)=O)O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)N3C=CC(=O)NC3=O
OpenEye OEToolkits 1.5.0C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)(O)O[P@@](=O)(O)O[C@@H]3[C@@H]([C@H]([C@@H]([C@H](O3)C(=O)O)O)O)O)O)O
CACTVS 3.341O[C@@H]1[C@@H](O)[C@H](O[C@@H]([C@H]1O)C(O)=O)O[P@@](O)(=O)O[P@@](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N3C=CC(=O)NC3=O
OpenEye OEToolkits 1.5.0C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OC3C(C(C(C(O3)C(=O)O)O)O)O)O)O
FormulaC15 H22 N2 O18 P2
NameURIDINE-5'-DIPHOSPHATE-GLUCURONIC ACID;
UDP-GLUCURONIC ACID
ChEMBLCHEMBL228057
DrugBankDB03041
ZINCZINC000008215691
PDB chain6h0p Chain A 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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PDB6h0p Deciphering the enzymatic mechanism of sugar ring contraction in UDP-apiose biosynthesis.
Resolution3.47 Å
Binding residue
(original residue number in PDB)		P102 Y105 T139 E141 R182 Y185 N214 R235 V236 C239 F240 V253 R260 V298 F330 Y331 Y335 D337 R341
Binding residue
(residue number reindexed from 1)		P95 Y98 T132 E134 R175 Y178 N207 R228 V229 C232 F233 V246 R253 V291 F323 Y324 Y328 D330 R334
Annotation score4
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

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6h0p, PDBe:6h0p, PDBj:6h0p
PDBsum6h0p
PubMed31844840
UniProtQ9ZUY6|AXS1_ARATH UDP-D-apiose/UDP-D-xylose synthase 1 (Gene Name=AXS1)

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