Structure of PDB 2dy3 Chain A Binding Site BS01

Receptor Information
>2dy3 Chain A (length=338) Species: 1718 (Corynebacterium glutamicum) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MNLLTTKIDLDAIAHNTRVLKQMAGPAKLMAVVKANAYNHGVEKVAPVIA
AHGADAFGVATLAEAMQLRDIGISQEVLCWIWTPEQDFRAAIDRNIDLAV
ISPAHAKALIETDAEHIRVSIKIDSGLHRSGVDEQEWEGVFSALAAAPHI
EVTGMFTHLAETDRQIIAFRRALALARKHGLECPVNHVCNSPAFLTRSDL
HMEMVRPGLAFYGLEPVAGLEHGLKPAMTWEAKVSVVKQIERGFVAVVPA
GYADGMPRHAQGKFSVTIDGLDYPQVGRVCMDQFVISLGDNPHGVEAGAK
AVIFGENGHDATDFAERLDTINYEVVCRPTGRTVRAYV
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 chain2dy3 Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2dy3 Crystal Structure of Alanine Racemase from Corynebacterium glutamicum at 2.1 A resolution
Resolution2.1 Å
Binding residue
(original residue number in PDB)		V32 K34 Y38 W80 H158 N198 S199 R214 G216 L217 Y346
Binding residue
(residue number reindexed from 1)		V32 K34 Y38 W80 H158 N190 S191 R206 G208 L209 Y323
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) K34 R129 H158 R214 C303 D305
Catalytic site (residue number reindexed from 1) K34 R129 H158 R206 C280 D282
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
Biological Process
GO:0006522 alanine metabolic process
GO:0009252 peptidoglycan biosynthetic process
GO:0030632 D-alanine biosynthetic process
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:2dy3, PDBe:2dy3, PDBj:2dy3
PDBsum2dy3
PubMed
UniProtQ8RSU9|ALR_CORGL Alanine racemase (Gene Name=alr)

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