Structure of PDB 1yxd Chain A Binding Site BS02

Receptor Information
>1yxd Chain A (length=292) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MFTGSIVAIVTPMDEKGNVCRASLKKLIDYHVASGTSAIVSVGTTGESAT
LNHDEHADVVMMTLDLADGRIPVIAGTGANATAEAISLTQRFNDSGIVGC
LTVTPYYNRPSQEGLYQHFKAIAEHTDLPQILYNVPSRTGCDLLPETVGR
LAKVKNIIGIKEATGNLTRVNQIKELVSDDFVLLSGDDASALDFMQLGGH
GVISVTANVAARDMAQMCKLAAEGHFAEARVINQRLMPLHNKLFVEPNPI
PVKWACKELGLVATDTLRLPMTPITDSGRETVRAALKHAGLL
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 chain1yxd Chain B Residue 2300 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1yxd The crystal structures of native and (S)-lysine-bound dihydrodipicolinate synthase from Escherichia coli with improved resolution show new features of biological significance.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		N80 E84
Binding residue
(residue number reindexed from 1)		N80 E84
Annotation score2
Binding affinityPDBbind-CN: -logKd/Ki=5.30,Ki=5uM
Enzymatic activity
Catalytic site (original residue number in PDB) T44 Y107 Y133 R138 K161 I203
Catalytic site (residue number reindexed from 1) T44 Y107 Y133 R138 K161 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
GO:0042802 identical protein binding
Biological Process
GO:0009085 lysine biosynthetic process
GO:0009089 lysine biosynthetic process via diaminopimelate
GO:0019877 diaminopimelate biosynthetic process
GO:0044281 small molecule metabolic process
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1yxd, PDBe:1yxd, PDBj:1yxd
PDBsum1yxd
PubMed16041077
UniProtP0A6L2|DAPA_ECOLI 4-hydroxy-tetrahydrodipicolinate synthase (Gene Name=dapA)

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