Structure of PDB 4l39 Chain A Binding Site BS01

Receptor Information
>4l39 Chain A (length=541) Species: 3702 (Arabidopsis thaliana) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ETFEKQLKDLTSNVKSIQDNLLEEIITPNTKTEYLQRFLIDRFDKELFKK
NVPIVSYEDIKPYLDRVVNGESSDVISARTITGFLLSAQKMMPWNNKYLD
NLTFIYDLRMQVITKHVKGVEEGKGMMFLFTKQESMTPSGLPARVATSSY
FKSDYFKNRPSNWYYSYTSPDEVILCPNNTESLYCHLLCGLVQRDEVVRT
GSIFASVMVRAIEVLKNSWEELCSNIRSGHLSNWVTDLGCQNSVSLVLGG
PRPELADTIEEICNQNSWKGIVKRLWPNTKYIETVVTGSMGQYVPMLNYY
CNDLPLVSTTYGSSETTFGINLDPLCKPEDVSYTFMPNMSYFEFIPMDGG
DKNDVVDLEDVKLGCTYEPVVTNFAGLYRMRVGDIVLVTGFYNNAPQFKF
VRRENVVLSIDSDKTNEEDLFKAVSQAKLVLESSGLDLKDFTSYADTSTF
PGHYVVYLEGEQFELDEEALSTCCLVMEESLDNVYKRCRFKDGSIGPLEI
RVVGTFDSLMDFFISQGQYKTPRCKALQVLETCVVAKFFSI
Ligand information
Ligand IDAPC
InChIInChI=1S/C11H18N5O12P3/c12-9-6-10(14-2-13-9)16(3-15-6)11-8(18)7(17)5(27-11)1-26-29(19,20)4-30(21,22)28-31(23,24)25/h2-3,5,7-8,11,17-18H,1,4H2,(H,19,20)(H,21,22)(H2,12,13,14)(H2,23,24,25)/t5-,7-,8-,11-/m1/s1
InChIKeyCAWZRIXWFRFUQB-IOSLPCCCSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(C[P@](=O)(O)OP(=O)(O)O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)C[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(CP(=O)(O)OP(=O)(O)O)O)O)O)N
ACDLabs 10.04O=P(O)(O)OP(=O)(O)CP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)C[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
FormulaC11 H18 N5 O12 P3
NameDIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER;
ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL132722
DrugBankDB02596
ZINCZINC000008295117
PDB chain4l39 Chain A Residue 603 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB4l39 Determination of the GH3.12 protein conformation through HPLC-integrated SAXS measurements combined with X-ray crystallography.
Resolution2.81 Å
Binding residue
(original residue number in PDB)		S95 V299 T301 T324 Y325 G326 S327 S328 Y347 D398 F414
Binding residue
(residue number reindexed from 1)		S87 V285 T287 T310 Y311 G312 S313 S314 Y333 D384 F400
Annotation score1
Enzymatic activity
Enzyme Commision number 6.3.2.-
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0016874 ligase activity
GO:0052625 N-(4-aminobenzoyl)-L-glutamate synthetase activity
GO:0052626 N-benzoyl-L-glutamate synthetase activity
GO:0052627 N-vanillate-L-glutamate synthetase activity
GO:0052628 N-(4-hydroxybenzoyl)-L-glutamate synthetase activity
Biological Process
GO:0006952 defense response
GO:0009626 plant-type hypersensitive response
GO:0009863 salicylic acid mediated signaling pathway
GO:0010112 regulation of systemic acquired resistance
GO:0016046 detection of fungus
GO:0018874 benzoate metabolic process
GO:0034052 positive regulation of plant-type hypersensitive response
GO:0042742 defense response to bacterium
GO:0071456 cellular response to hypoxia

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4l39, PDBe:4l39, PDBj:4l39
PDBsum4l39
PubMed24100325
UniProtQ9LYU4|GH312_ARATH 4-substituted benzoates-glutamate ligase GH3.12 (Gene Name=GH3.12)

[Back to BioLiP]