Structure of PDB 6h0p Chain B Binding Site BS01

Receptor Information
>6h0p Chain B (length=367) Species: 3702 (Arabidopsis thaliana) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VDLDGKPIQPLTICMIGAGGFIGSHLCEKLLTETPHKVLALDVYNDKIKH
LLERIQFHRINIKHDSRLEGLVKMADLIINLAAIATPADYNTRPLDTIYS
NFIDALPVVKYCSENNKRLIHFSTCEVYGKTIGSFLPKDHPLRDDPAFYV
LKEDISPCIFGSIEKQRWSYACAKQLIERLVYAEGAENGLEFTIVRPFNW
IGPRMDFIPGIDGPSEGVPRVLACFSNNLLRREPLKLVDGGESQRTFVYI
NDAIEAVLLMIENPERANGHIFNVGNPNNEVTVRQLAEMMTEVYAKVSGE
GAIESPTVDVSSKEFYGEGYDDSDKRIPDMTIINRQLGWNPKTSLWDLLE
STLTYQHRTYAEAVKKA
Ligand information
Ligand IDNAD
InChIInChI=1S/C21H27N7O14P2/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(32)14(30)11(41-21)6-39-44(36,37)42-43(34,35)38-5-10-13(29)15(31)20(40-10)27-3-1-2-9(4-27)18(23)33/h1-4,7-8,10-11,13-16,20-21,29-32H,5-6H2,(H5-,22,23,24,25,33,34,35,36,37)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyBAWFJGJZGIEFAR-NNYOXOHSSA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC(=O)c1ccc[n+](c1)[C@@H]2O[C@H](CO[P]([O-])(=O)O[P@](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)N
CACTVS 3.341NC(=O)c1ccc[n+](c1)[CH]2O[CH](CO[P]([O-])(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
OpenEye OEToolkits 1.5.0c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)([O-])O[P@@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)N
FormulaC21 H27 N7 O14 P2
NameNICOTINAMIDE-ADENINE-DINUCLEOTIDE
ChEMBLCHEMBL1234613
DrugBankDB14128
ZINC
PDB chain6h0p Chain B Residue 401 [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)		G24 G27 F28 I29 D49 N76 I77 L96 A97 A98 F137 Y185 K189
Binding residue
(residue number reindexed from 1)		G17 G20 F21 I22 D42 N61 I62 L81 A82 A83 F122 Y170 K174
Annotation score1
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
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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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