Structure of PDB 3b8u Chain B Binding Site BS01

Receptor Information
>3b8u Chain B (length=358) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QAATVVINRRALRHNLQRLRELAPASKMVAVVKANAYGHGLLETARTLPD
ADAFGVARLEEALRLRAGGITKPVLLLEGFFDARDLPTISAQHFHTAVHN
EEQLAALEEASLDEPVTVWMKLDTGMHRLGVRPEQAEAFYHRLTQCKNVR
QPVNIVSHFARADEPKCGATEKQLAIFNTFCEGKPGQRSIAASGGILLWP
QSHFDWVRPGIILYGVSPLADRSTGADFGCQPVMSLTSSLIAVREHKAGE
PVGYGGTWVSERDTRLGVVAMGYGDGYPRAAPSGTPVLVNGREVPIVGRV
AMDMICVDLGPQAQDKAGDPVILWGEGLPVERIAEMTKVSAYELITRLTS
RVAMKYVD
Ligand information
Ligand IDPLP
InChIInChI=1S/C8H10NO6P/c1-5-8(11)7(3-10)6(2-9-5)4-15-16(12,13)14/h2-3,11H,4H2,1H3,(H2,12,13,14)
InChIKeyNGVDGCNFYWLIFO-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Cc1ncc(CO[P](O)(O)=O)c(C=O)c1O
OpenEye OEToolkits 1.5.0Cc1c(c(c(cn1)COP(=O)(O)O)C=O)O
ACDLabs 10.04O=P(O)(O)OCc1cnc(c(O)c1C=O)C
FormulaC8 H10 N O6 P
NamePYRIDOXAL-5'-PHOSPHATE;
VITAMIN B6 Phosphate
ChEMBLCHEMBL82202
DrugBankDB00114
ZINCZINC000001532514
PDB chain3b8u Chain B Residue 1001 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3b8u Residues Asp164 and Glu165 at the substrate entryway function potently in substrate orientation of alanine racemase from E. coli: Enzymatic characterization with crystal structure analysis
Resolution3.0 Å
Binding residue
(original residue number in PDB)		V32 K34 Y38 H159 A193 S194 R209 G211 I212 Y343
Binding residue
(residue number reindexed from 1)		V31 K33 Y37 H158 A192 S193 R208 G210 I211 Y342
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) K34 R129 H159 R209 Y255 A302 D304
Catalytic site (residue number reindexed from 1) K33 R128 H158 R208 Y254 A301 D303
Enzyme Commision number 5.1.1.1: alanine racemase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0008784 alanine racemase activity
GO:0016853 isomerase activity
GO:0030170 pyridoxal phosphate binding
GO:0042803 protein homodimerization activity
Biological Process
GO:0006522 alanine metabolic process
GO:0008360 regulation of cell shape
GO:0009252 peptidoglycan biosynthetic process
GO:0030632 D-alanine biosynthetic process
GO:0071555 cell wall organization
Cellular Component
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:3b8u, PDBe:3b8u, PDBj:3b8u
PDBsum3b8u
PubMed18434499
UniProtP0A6B4|ALR1_ECOLI Alanine racemase, biosynthetic (Gene Name=alr)

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