2Y2B	crystal structure of AmpD in complex with reaction products	date
authors	Carrasco-Lopez, C., Rojas-Altuve, A., Zhang, W., Hesek, D., Lee, M., Barbe, S., Andre, I., Silva-Martin, N., Martinez-Ripoll, M., Mobashery, S., Hermoso, J.A.
compound		source
symmetry		R_factor R_Free 0.2235
crystal cell	length a length b length c angle alpha angle beta angle gamma
method	X-Ray Diffraction	resolution	1.90
ligand	AH0, MHI, ZN	enzyme
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] (101 Kb) [Save to disk] Biological Unit Coordinates (2y2b.pdb1.gz) 35 Kb Biological Unit Coordinates (2y2b.pdb2.gz) 33 Kb Biological Unit Coordinates (2y2b.pdb3.gz) 33 Kb LPC: Ligand-Protein Contacts for 2Y2B CSU: Contacts of Structural Units for 2Y2B Structure Factors (652 Kb) Retrieve 2Y2B in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2Y2B from S2C, [Save to disk] Re-refined 2y2b structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2Y2B 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 2Y2B

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 2Y2B, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2y2b_C] [2y2b] [2y2b_B] [2y2b_A] SWISS-PROT database: Domain organization of by SWISSPFAM Domain found in 2Y2B: [Ami_2 ] by SMART

Other resources with information on 2Y2B

Community annotation for 2Y2B at PDBWiki (http://pdbwiki.org)

Movements, Movies and Images

Images from IMB Jena Image Library of Biological Macromolecules.

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