2Y2D	Hydrolase	date	Dec 14, 2010
title	Crystal Structure Of Ampd Holoenzyme
authors	C.Carrasco-Lopez, A.Rojas-Altuve, W.Zhang, D.Hesek, M.Lee, S.Barb I.Andre, N.Silva-Martin, M.Martinez-Ripoll, S.Mobashery, J.A.He
compound		source
Molecule: 1,6-Anhydro-N-Acetylmuramyl-L-Alanine Amidase Amp Chain: A, B, C Synonym: Ampd, N-Acetylmuramoyl-L-Alanine Amidase Ec: 3.5.1.28 Engineered: Yes		Organism_scientific: Citrobacter Freundii Organism_taxid: 546 Expression_system: Escherichia Coli Expression_system_taxid: 562
symmetry	Space Group: P 32	R_factor 0.206 R_Free 0.278
crystal cell	length a length b length c angle alpha angle beta angle gamma 67.691 67.691 92.805 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	2.00 Å
ligand	ZN	enzyme	Hydrolase E.C.3.5.1.28 BRENDA
Gene Ontology	Chain Function Process Component A, C, B
Primary reference	Crystal Structures of Bacterial Peptidoglycan Amidase AmpD and an Unprecedented Activation Mechanism., Carrasco-Lopez C, Rojas-Altuve A, Zhang W, Hesek D, Lee M, Barbe S, Andre I, Ferrer P, Silva-Martin N, Castro GR, Martinez-Ripoll M, Mobashery S, Hermoso JA, J Biol Chem. 2011 Sep 9;286(36):31714-22. Epub 2011 Jul 20. PMID:21775432

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (106 Kb) [Save to disk] Biological Unit Coordinates (2y2d.pdb1.gz) 35 Kb Biological Unit Coordinates (2y2d.pdb2.gz) 35 Kb Biological Unit Coordinates (2y2d.pdb3.gz) 34 Kb LPC: Ligand-Protein Contacts for 2Y2D CSU: Contacts of Structural Units for 2Y2D Structure Factors (461 Kb) Retrieve 2Y2D in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2Y2D from S2C, [Save to disk] Re-refined 2y2d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2Y2D in 3D

Proteopedia, because life has more than 2D. On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure. On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.

Visual 3D analysis of 2Y2D

Ramachandran plot from PDBSum

Structure-derived information

Electron Density related parameters from EDS Electron Density Server, at Upsala Dipole moment, from Dipole Server at Weizmann Institute 3D motif for 2Y2D, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2y2d_B] [2y2d_A] [2y2d_C] [2y2d] SWISS-PROT database: Domain organization of by SWISSPFAM Domain found in 2Y2D: [Ami_2 ] by SMART

Other resources with information on 2Y2D

Community annotation for 2Y2D at PDBWiki (http://pdbwiki.org)

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