Structure of PDB 1ikg Chain A Binding Site BS01

Receptor Information
>1ikg Chain A (length=345) Species: 31952 (Streptomyces sp. R61) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LPAPDDTGLQAVLHTALSQGAPGAMVRVDDNGTIHQLSEGVADRATGRAI
TTTDRFRVGSVTKSFSAVVLLQLVDEGKLDLDASVNTYLPGLLPDDRITV
RQVMSHRSGLYDYTNDMFAQTVPGFESVRNKVFSYQDLITLSLKHGVTNA
PGAAYSYSNTNFVVAGMLIEKLTGHSVATEYQNRIFTPLNLTDTFYVHPD
TVIPGTHANGYLTPDEAGGALVDSTEQTVSWAQSAGAVISSTQDLDTFFS
ALMSGQLMSAAQLAQMQQWTTVNSTQGYGLGLRRRDLSCGISVYGHTGTV
QGYYTYAFASKDGKRSVTALANTSNNVNVLNTMARTLESAFCGKP
Ligand information
Ligand IDREX
InChIInChI=1S/C15H26N4O7/c1-8(13(22)18-9(2)14(23)24)17-11(20)6-4-3-5-10(15(25)26)19-12(21)7-16/h8-10H,3-7,16H2,1-2H3,(H,17,20)(H,18,22)(H,19,21)(H,23,24)(H,25,26)/t8-,9-,10+/m1/s1
InChIKeyRALBRZJHHGWNNU-BBBLOLIVSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C[C@H](C(=O)N[C@H](C)C(=O)O)NC(=O)CCCC[C@@H](C(=O)[O-])NC(=O)C[NH3+]
CACTVS 3.341C[CH](NC(=O)[CH](C)NC(=O)CCCC[CH](NC(=O)C[NH3+])C([O-])=O)C(O)=O
CACTVS 3.341C[C@@H](NC(=O)[C@@H](C)NC(=O)CCCC[C@H](NC(=O)C[NH3+])C([O-])=O)C(O)=O
ACDLabs 10.04O=C(NC(C(=O)O)C)C(NC(=O)CCCCC(C([O-])=O)NC(=O)C[NH3+])C
OpenEye OEToolkits 1.5.0CC(C(=O)NC(C)C(=O)O)NC(=O)CCCCC(C(=O)[O-])NC(=O)C[NH3+]
FormulaC15 H26 N4 O7
NameGLYCYL-L-ALPHA-AMINO-EPSILON-PIMELYL-D-ALANYL-D-ALANINE
ChEMBL
DrugBankDB02578
ZINCZINC000015599994
PDB chain1ikg Chain A Residue 400 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB1ikg Structures of two kinetic intermediates reveal species specificity of penicillin-binding proteins.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		S62 F120 T123 Y159 N161 W233 R285 H298 T299 G300 T301 Q303 S326 N327
Binding residue
(residue number reindexed from 1)		S60 F118 T121 Y157 N159 W231 R283 H296 T297 G298 T299 Q301 S324 N325
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) S62 K65 D114 T116 V130 Y159 N161 V165 T227 H298 G304
Catalytic site (residue number reindexed from 1) S60 K63 D112 T114 V128 Y157 N159 V163 T225 H296 G302
Enzyme Commision number 3.4.16.4: serine-type D-Ala-D-Ala carboxypeptidase.
Gene Ontology
Molecular Function
GO:0004180 carboxypeptidase activity
GO:0009002 serine-type D-Ala-D-Ala carboxypeptidase activity
Biological Process
GO:0006508 proteolysis
GO:0008360 regulation of cell shape
GO:0009252 peptidoglycan biosynthetic process
GO:0071555 cell wall organization
Cellular Component
GO:0005576 extracellular region

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1ikg, PDBe:1ikg, PDBj:1ikg
PDBsum1ikg
PubMed12215418
UniProtP15555|DAC_STRSR D-alanyl-D-alanine carboxypeptidase

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