Structure of PDB 3co8 Chain B Binding Site BS01

Receptor Information
>3co8 Chain B (length=345) Species: 203123 (Oenococcus oeni PSU-1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RSTRIEFSKSSLAYNVQYTKQVSGAKTLWLAVKSNAYGHGLLQVSKIARE
CGVDGLAVSVLDEGIAIRQAGIDDFILILGPIDVKYAPIASKYHFLTTVS
SLDWLKSADKILGKEKLSVNLAVDTGMNRIGVRSKKDLKDEIEFLQEHSD
HFSYDGIFTHFASSDNPDDHYFQRQKNRWYELIDGLIMPRYVHVMNSGAA
MYHSKELPGCNSIARVGTVVYGVEPSEGVLGPIDKLKPVFELKSALTFVK
KWIGTLPIGYGDGWLAEYQDFQLLIDGQKCRQVGQIAMDQMMVALPHEYP
IGTEVTLIGKSGKYENTLYDLHKHSGVPPWKITVAFSDRLKRMVV
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 chain3co8 Chain B Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB3co8 Structure of alanine racemase from Oenococcus oeni with bound pyridoxal 5'-phosphate.
Resolution1.7 Å
Binding residue
(original residue number in PDB)		K39 Y43 L85 R135 H166 S203 R221 G223 T224
Binding residue
(residue number reindexed from 1)		K33 Y37 L79 R129 H160 S197 R215 G217 T218
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) K39 R135 H166 R221 A312 D314
Catalytic site (residue number reindexed from 1) K33 R129 H160 R215 A287 D289
Enzyme Commision number 5.1.1.5: lysine racemase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0008784 alanine racemase activity
GO:0016853 isomerase activity
GO:0018113 lysine racemase 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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3co8, PDBe:3co8, PDBj:3co8
PDBsum3co8
PubMed23295479
UniProtQ04HB7|LYSR_OENOB Lysine racemase (Gene Name=OEOE_0162)

[Back to BioLiP]