Structure of PDB 4dpq Chain A Binding Site BS01

Receptor Information
>4dpq Chain A (length=307) Species: 3702 (Arabidopsis thaliana) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NTDDIKALRVITAIKTPYLPDGRFDLEAYDDLVNIQIQNGAEGVIVGGTT
GEGQLMSWDEHIMLIGHTVNCFGGSIKVIGNTGSNSTREAIHATEQGFAV
GMHAALHINPYYGKTSIEGLIAHFQSVLHMGPTIIYNVPGRTGQDIPPRA
IFKLSQNPNLAGVKECVGNKRVEEYTENGVVVWSGNDDECHDSRWDYGAT
GVISVTSNLVPGLMRKLMFEGRNSSLNSKLLPLMAWLFHEPNPIGINTAL
AQLGVSRPVFRLPYVPLPLSKRLEFVKLVKEIGREHFVGEKDVQALDDDD
FILIGRY
Ligand information
Ligand IDLYS
InChIInChI=1S/C6H14N2O2/c7-4-2-1-3-5(8)6(9)10/h5H,1-4,7-8H2,(H,9,10)/p+1/t5-/m0/s1
InChIKeyKDXKERNSBIXSRK-YFKPBYRVSA-O
SMILES
SoftwareSMILES
CACTVS 3.341N[CH](CCCC[NH3+])C(O)=O
ACDLabs 10.04O=C(O)C(N)CCCC[NH3+]
OpenEye OEToolkits 1.5.0C(CC[NH3+])C[C@@H](C(=O)O)N
CACTVS 3.341N[C@@H](CCCC[NH3+])C(O)=O
OpenEye OEToolkits 1.5.0C(CC[NH3+])CC(C(=O)O)N
FormulaC6 H15 N2 O2
NameLYSINE
ChEMBL
DrugBank
ZINC
PDB chain4dpq Chain A Residue 404 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4dpq Characterisation of the first enzymes committed to lysine biosynthesis in Arabidopsis thaliana
Resolution2.202 Å
Binding residue
(original residue number in PDB)		G111 Q112 M114 W116 H119 Y169
Binding residue
(residue number reindexed from 1)		G53 Q54 M56 W58 H61 Y111
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) T107 Y170 Y194 R199 K222 I261
Catalytic site (residue number reindexed from 1) T49 Y112 Y136 R141 K164 I203
Enzyme Commision number 4.3.3.7: 4-hydroxy-tetrahydrodipicolinate synthase.
Gene Ontology
Molecular Function
GO:0008840 4-hydroxy-tetrahydrodipicolinate synthase activity
GO:0016829 lyase activity
Biological Process
GO:0009085 lysine biosynthetic process
GO:0009089 lysine biosynthetic process via diaminopimelate
GO:0019877 diaminopimelate biosynthetic process
Cellular Component
GO:0009507 chloroplast

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4dpq, PDBe:4dpq, PDBj:4dpq
PDBsum4dpq
PubMed22792278
UniProtQ9FVC8|DAPA2_ARATH 4-hydroxy-tetrahydrodipicolinate synthase 2, chloroplastic (Gene Name=DHDPS2)

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