Structure of PDB 2y2b Chain A Binding Site BS01

Receptor Information
>2y2b Chain A (length=179) Species: 546 (Citrobacter freundii) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MLLDEGWLAEARRVPSPHYDCRPDDENPSLLVVHNISLPPGEFGGPWIDA
LFTGTIDPNAHPYFAGIAHLRVSAHCLIRRDGEIVQYVPFDKRAWHAGVS
SYQGRERCNDFSIGIELEGTDTLAYTDAQYQQLAAVTNALITRYPAIANN
MTGHCNIAPERKTDPGPSFDWARFRALVT
Ligand information
Ligand IDAH0
InChIInChI=1S/C11H17NO7/c1-4(10(15)16)18-9-7(12-5(2)13)11-17-3-6(19-11)8(9)14/h4,6-9,11,14H,3H2,1-2H3,(H,12,13)(H,15,16)/t4-,6-,7-,8-,9-,11-/m1/s1
InChIKeyZFEGYUMHFZOYIY-YVNCZSHWSA-N
SMILES
SoftwareSMILES
CACTVS 3.341C[CH](O[CH]1[CH](O)[CH]2CO[CH](O2)[CH]1NC(C)=O)C(O)=O
CACTVS 3.341C[C@@H](O[C@H]1[C@H](O)[C@H]2CO[C@H](O2)[C@@H]1NC(C)=O)C(O)=O
OpenEye OEToolkits 1.5.0CC(C(=O)O)OC1C(C2OCC(C1O)O2)NC(=O)C
OpenEye OEToolkits 1.5.0C[C@H](C(=O)O)O[C@@H]1[C@H]([C@@H]2OC[C@H]([C@H]1O)O2)NC(=O)C
ACDLabs 10.04O=C(O)C(OC2C(O)C1OC(OC1)C2NC(=O)C)C
FormulaC11 H17 N O7
Name2-(2-ACETYLAMINO-4-HYDROXY-6,8-DIOXA-BICYCLO[3.2.1]OCT-3-YLOXY)-PROPIONIC ACID;
1,6-anhydro-N-acetylmuramic acid
ChEMBL
DrugBank
ZINCZINC000034118661
PDB chain2y2b Chain A Residue 201 [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]
PDB2y2b Crystal Structures of Bacterial Peptidoglycan Amidase Ampd and an Unprecedented Activation Mechanism.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		N35 I36 L38 L51 Y63 K162 D164
Binding residue
(residue number reindexed from 1)		N35 I36 L38 L51 Y63 K162 D164
Annotation score1
Enzymatic activity
Enzyme Commision number 3.5.1.28: N-acetylmuramoyl-L-alanine amidase.
Gene Ontology
Molecular Function
GO:0008745 N-acetylmuramoyl-L-alanine amidase activity
GO:0016787 hydrolase activity
GO:0046872 metal ion binding
Biological Process
GO:0009253 peptidoglycan catabolic process
GO:0009254 peptidoglycan turnover
GO:0071555 cell wall organization
Cellular Component
GO:0005737 cytoplasm

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:2y2b, PDBe:2y2b, PDBj:2y2b
PDBsum2y2b
PubMed21775432
UniProtP82974|AMPD_CITFR 1,6-anhydro-N-acetylmuramyl-L-alanine amidase AmpD (Gene Name=ampD)

[Back to BioLiP]