Structure of PDB 3ly0 Chain A Binding Site BS01

Receptor Information
>3ly0 Chain A (length=351) Species: 272943 (Cereibacter sphaeroides 2.4.1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DTIPVFDGHNDFLLRLLRNPANRETIWLKGDGTGHLDLPRMKEGGFAGGF
FAIYVPSPQAHDAAHFEAMMDAPPFELPLPPMIRAEQAQPVALAMAGHLL
WMERAARGRFKVCRTAAEVRSCHADGIVSGIMHMEGAEAIGADLDALHLF
HSLGLRSLGPVWSRPTVFGHGVPFRFPGSPDTGEGLTEAGRRLVAECNRL
KIMLDLSHLNEKGFDDVARLSDAPLVATHSNAHAVTPSTRNLTDRQLAMI
RESRGMVGLNFATSFLREDGRRSAEMGWEPVLRHLDHLIDRLGEDHVGMG
SDFDGATIPQGIADVTGLPALQAAMRAHGYDEPLMRKLCHENWYGLLERT
W
Ligand information
Ligand IDLY0
InChIInChI=1S/C6H14NO4P/c1-4(6(8)9)3-12(10,11)5(2)7/h4-5H,3,7H2,1-2H3,(H,8,9)(H,10,11)/t4-,5+/m0/s1
InChIKeyXXVGIEKADYFHOF-CRCLSJGQSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0C[C@@H](C[P@](=O)([C@H](C)N)O)C(=O)O
CACTVS 3.352C[CH](N)[P](O)(=O)C[CH](C)C(O)=O
CACTVS 3.352C[C@H](N)[P](O)(=O)C[C@H](C)C(O)=O
OpenEye OEToolkits 1.7.0CC(CP(=O)(C(C)N)O)C(=O)O
FormulaC6 H14 N O4 P
Name(2R)-3-[(R)-[(1R)-1-aminoethyl](hydroxy)phosphoryl]-2-methylpropanoic acid
ChEMBL
DrugBank
ZINCZINC000025109103
PDB chain3ly0 Chain A Residue 363 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3ly0 Crystal structure of metallo peptidase from Rhodobacter sphaeroides liganded with phosphinate mimic of dipeptide L-Ala-D-Ala
Resolution1.399 Å
Binding residue
(original residue number in PDB)		D13 Y56 H63 E137 W164 F176 H210 H231 R242 F267 D304 G307
Binding residue
(residue number reindexed from 1)		D11 Y54 H61 E135 W162 F174 H208 H229 R240 F265 D302 G305
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) H11 D13 E137 W164 H210 H231 D304
Catalytic site (residue number reindexed from 1) H9 D11 E135 W162 H208 H229 D302
Enzyme Commision number 3.4.13.19: membrane dipeptidase.
Gene Ontology
Molecular Function
GO:0016805 dipeptidase activity
GO:0046872 metal ion binding
GO:0070573 metallodipeptidase activity
Biological Process
GO:0006508 proteolysis

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3ly0, PDBe:3ly0, PDBj:3ly0
PDBsum3ly0
PubMed
UniProtQ3IZQ3

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