Structure of PDB 4pfm Chain B Binding Site BS01

Receptor Information
>4pfm Chain B (length=295) Species: 314608 (Shewanella benthica KT99) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HMINGSIVALITPLNSDGTVDYTSLEKLVEYHITEGTDAIVAVGTTGESA
TLPISEHIAVVGQTVKFASGRIPVIGGNGANATAEAIELTKAQNKLGVAA
MLGVTPYYNKPSPKGLIAHYTAVAASTDIPQILYNVPGRTAVDMLPETIA
QLVEVPNIIGVKDATGDVARVKQLRDLCGNDFLLYSGDDATAREFLTLGG
DGVISVANNIVPKLFKLMCDAALAGDTQAAMAAEDQIKGLFSALFCEANP
IPVKWAAHKMGLISQGDIRLPLTELSTEFHGLLLDAMKNARIEVK
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 chain4pfm Chain A Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4pfm Defining a Molecular Determinant of Lysine-Mediated Allosteric Inhibition of DHDPS.
Resolution2.327 Å
Binding residue
(original residue number in PDB)		N80 E84
Binding residue
(residue number reindexed from 1)		N81 E85
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) T44 Y107 Y133 R138 K161 I203
Catalytic site (residue number reindexed from 1) T45 Y108 Y134 R139 K162 I204
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
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:4pfm, PDBe:4pfm, PDBj:4pfm
PDBsum4pfm
PubMed
UniProtA9DKW4

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