Structure of PDB 2y2d Chain B Binding Site BS01

Receptor Information

>2y2d Chain B (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 ID

InChI

InChI=1S/Zn/q+2

InChIKey

PTFCDOFLOPIGGS-UHFFFAOYSA-N

SMILES

Software	SMILES
CACTVS 3.341	[Zn++]
ACDLabs 10.04 OpenEye OEToolkits 1.5.0	[Zn+2]

Formula

Name

ZINC ION

PDB chain

2y2d Chain B Residue 1180 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	2y2d Crystal Structures of Bacterial Peptidoglycan Amidase Ampd and an Unprecedented Activation Mechanism.
Resolution	2.0 Å
Binding residue (original residue number in PDB)	H34 H154 D164
Binding residue (residue number reindexed from 1)	H34 H154 D164
Annotation score	4

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

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Cellular Component

External links

PDB	RCSB:2y2d, PDBe:2y2d, PDBj:2y2d
PDBsum	2y2d
PubMed	21775432
UniProt	P82974\|AMPD_CITFR 1,6-anhydro-N-acetylmuramyl-L-alanine amidase AmpD (Gene Name=ampD)

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