Structure of PDB 3ei6 Chain B Binding Site BS02

Receptor Information
>3ei6 Chain B (length=411) 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
SKYAGFTGVRLGWTVIPKKLLYSDGFPVAKDFNRIICTCFNGASNISQAG
ALACLTPEGLEAMHKVIGFYKENTNIIIDTFTSLGYDVYGGKNAPYVWVH
FPNQSSWDVFAEILEKTHVVTTPGSGFGPGGEGFVRVSAFGHRENILEAC
RRFKQLYKHHH
Ligand information
Ligand IDPL4
InChIInChI=1S/C15H24N3O9P/c1-8-13(19)10(9(5-17-8)7-27-28(24,25)26)6-18-12(15(22)23)4-2-3-11(16)14(20)21/h5,11-12,18-19H,2-4,6-7,16H2,1H3,(H,20,21)(H,22,23)(H2,24,25,26)/t11-,12-/m0/s1
InChIKeyAEPLLCAFHXWECU-RYUDHWBXSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C(O)C(N)CCCC(C(=O)O)NCc1c(cnc(c1O)C)COP(=O)(O)O
OpenEye OEToolkits 1.5.0Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@@H](CCC[C@@H](C(=O)O)N)C(=O)O)O
OpenEye OEToolkits 1.5.0Cc1c(c(c(cn1)COP(=O)(O)O)CNC(CCCC(C(=O)O)N)C(=O)O)O
CACTVS 3.341Cc1ncc(CO[P](O)(O)=O)c(CN[C@@H](CCC[C@H](N)C(O)=O)C(O)=O)c1O
CACTVS 3.341Cc1ncc(CO[P](O)(O)=O)c(CN[CH](CCC[CH](N)C(O)=O)C(O)=O)c1O
FormulaC15 H24 N3 O9 P
Name(2S,6S)-2-amino-6-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]heptanedioic acid
ChEMBL
DrugBank
ZINCZINC000058660314
PDB chain3ei6 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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PDB3ei6 Mechanism of substrate recognition and PLP-induced conformational changes in LL-diaminopimelate aminotransferase from Arabidopsis thaliana.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		Y37 F39 G64 G127 A128 K129 Y152 N209 D237 Y240 S267 S269 R278 R404
Binding residue
(residue number reindexed from 1)		Y19 F21 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:3ei6, PDBe:3ei6, PDBj:3ei6
PDBsum3ei6
PubMed18952095
UniProtQ93ZN9|DAPAT_ARATH LL-diaminopimelate aminotransferase, chloroplastic (Gene Name=DAP)

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