5CMS	Hydrolase	date	Jul 17, 2015
title	Structural Insights Into The Mechanism Of Escherichia Coli Y
authors	W.Zhang, C.Wang, Y.Song, C.Shao, X.Zhang, J.Zang
compound		source
Molecule: O-Acetyl-Adp-Ribose Deacetylase Chain: R, A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q Synonym: Regulator Of Rnase III Activity Ec: 3.5.1.- Engineered: Yes Mutation: Yes		Organism_scientific: Escherichia Coli Organism_taxid: 562 Gene: Ymdb Expression_system: Escherichia Coli Expression_system_taxid: 562
symmetry	Space Group: P 31 2 1	R_factor 0.222 R_Free 0.250
crystal cell	length a length b length c angle alpha angle beta angle gamma 290.019 290.019 114.324 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	2.98 Å
ligand	APR, SO4	enzyme	Hydrolase E.C.3.5.1 BRENDA
Gene Ontology	Chain Function Process Component F, N, K, E, Q, M, C, L, A, J, O, P, B, H, D, R, I, G
Primary reference	Structural insights into the mechanism of Escherichia coli YmdB: A 2'-O-acetyl-ADP-ribose deacetylase., Zhang W, Wang C, Song Y, Shao C, Zhang X, Zang J, J Struct Biol. 2015 Dec;192(3):478-86. doi: 10.1016/j.jsb.2015.10.010. Epub 2015 , Oct 19. PMID:26481419

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (479 Kb) [Save to disk] Biological Unit Coordinates (5cms.pdb1.gz) 32 Kb Biological Unit Coordinates (5cms.pdb2.gz) 32 Kb Biological Unit Coordinates (5cms.pdb3.gz) 33 Kb Biological Unit Coordinates (5cms.pdb4.gz) 33 Kb Biological Unit Coordinates (5cms.pdb5.gz) 33 Kb Biological Unit Coordinates (5cms.pdb6.gz) 32 Kb Biological Unit Coordinates (5cms.pdb7.gz) 32 Kb Biological Unit Coordinates (5cms.pdb8.gz) 32 Kb Biological Unit Coordinates (5cms.pdb9.gz) 33 Kb LPC: Ligand-Protein Contacts for 5CMS CSU: Contacts of Structural Units for 5CMS Structure Factors (2094 Kb) Retrieve 5CMS in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 5CMS from S2C, [Save to disk] Re-refined 5cms structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 5CMS 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 5CMS

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

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [5cms_O] [5cms_A] [5cms_B] [5cms_F] [5cms_K] [5cms_P] [5cms_N] [5cms] [5cms_J] [5cms_E] [5cms_R] [5cms_Q] [5cms_M] [5cms_H] [5cms_C] [5cms_G] [5cms_L] [5cms_I] [5cms_D] SWISS-PROT database: Domain organization of by SWISSPFAM Domain found in 5CMS: [A1pp ] by SMART

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