Structure of PDB 3ei9 Chain B Binding Site BS02

Receptor Information
>3ei9 Chain B (length=410) Species: 3702 (Arabidopsis thaliana) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EYKTKVSRNSNMSKLQAGYLFPEIARRRSAHLLKYPDAQVISLGIGDTTE
PIPEVITSAMAKKAHELSTIEGYSGYGAEQGAKPLRAAIAKTFYGGLGIG
DDDVFVSDGAKCDISRLQVMFGSNVTIAVQDPSYPAYVDSSVIMGQTGQF
NTDVQKYGNIEYMRCTPENGFFPDLSTVGRTDIIFFCSPNNPTGAAATRE
QLTQLVEFAKKNGSIIVYDSAYAMYMSDDNPRSIFEIPGAEEVAMETASF
SNYAGFTGVRLGWTVIPKKLLYSDGFPVAKDFNRIICTCFNGASNISQAG
ALACLTPEGLEAMHKVIGFYKENTNIIIDTFTSLGYDVYGGKNAPYVWVH
FPNQSSWDVFAEILEKTHVVTTPGSGFGPGGEGFVRVSAFGHRENILEAC
RRFKQLYKHH
Ligand information
Ligand IDPL6
InChIInChI=1S/C13H17N2O9P/c1-7-12(18)9(8(4-14-7)6-24-25(21,22)23)5-15-10(13(19)20)2-3-11(16)17/h4-5,10,18H,2-3,6H2,1H3,(H,16,17)(H,19,20)(H2,21,22,23)/b15-5+/t10-/m0/s1
InChIKeyZZRWFCMLYWHYGX-XSFFOXFNSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Cc1ncc(CO[P](O)(O)=O)c(C=N[C@@H](CCC(O)=O)C(O)=O)c1O
OpenEye OEToolkits 1.5.0Cc1c(c(c(cn1)COP(=O)(O)O)C=NC(CCC(=O)O)C(=O)O)O
OpenEye OEToolkits 1.5.0Cc1c(c(c(cn1)COP(=O)(O)O)\C=N\[C@@H](CCC(=O)O)C(=O)O)O
ACDLabs 10.04O=C(O)C(/N=C/c1c(cnc(c1O)C)COP(=O)(O)O)CCC(=O)O
CACTVS 3.341Cc1ncc(CO[P](O)(O)=O)c(C=N[CH](CCC(O)=O)C(O)=O)c1O
FormulaC13 H17 N2 O9 P
Name(E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-glutamic acid
ChEMBL
DrugBank
ZINCZINC000058651782
PDB chain3ei9 Chain B Residue 433 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3ei9 Mechanism of substrate recognition and PLP-induced conformational changes in LL-diaminopimelate aminotransferase from Arabidopsis thaliana.
Resolution1.55 Å
Binding residue
(original residue number in PDB)		Y37 F39 I63 G64 G127 A128 K129 Y152 N209 D237 Y240 S267 S269 R278 R404
Binding residue
(residue number reindexed from 1)		Y19 F21 I45 G46 G109 A110 K111 Y134 N191 D219 Y222 S249 S251 R260 R386
Annotation score1
Enzymatic activity
Enzyme Commision number 2.6.1.83: LL-diaminopimelate aminotransferase.
Gene Ontology
Molecular Function
GO:0005507 copper ion binding
GO:0008483 transaminase activity
GO:0010285 L,L-diaminopimelate aminotransferase activity
GO:0030170 pyridoxal phosphate binding
Biological Process
GO:0009058 biosynthetic process
GO:0009089 lysine biosynthetic process via diaminopimelate
GO:0009862 systemic acquired resistance, salicylic acid mediated signaling pathway
Cellular Component
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0009507 chloroplast
GO:0009570 chloroplast stroma

View graph for
Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3ei9, PDBe:3ei9, PDBj:3ei9
PDBsum3ei9
PubMed18952095
UniProtQ93ZN9|DAPAT_ARATH LL-diaminopimelate aminotransferase, chloroplastic (Gene Name=DAP)

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