2DCF	Hydrolase	date	Jan 06, 2006
title	Crystal Structure Of 6-Aminohexanoate-Dimer Hydrolase S112ag181dh266n Mutant With Substrate
authors	T.Ohki, N.Shibata, Y.Higuchi, M.Takeo, S.Negoro
compound		source
Molecule: 6-Aminohexanoate-Dimer Hydrolase Chain: A Ec: 3.5.1.46 Engineered: Yes Mutation: Yes		Organism_scientific: Flavobacterium Sp. Organism_taxid: 239 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Kp3998 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pkp1500
symmetry	Space Group: P 32 2 1	R_factor 0.183 R_Free 0.195
crystal cell	length a length b length c angle alpha angle beta angle gamma 96.620 96.620 112.600 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	1.40 Å
ligand	ACA, GOL, MES, SO4	enzyme	Hydrolase E.C.3.5.1.46 BRENDA
Gene Ontology	Chain Function Process Component A
Primary reference	Nylon-oligomer degrading enzyme/substrate complex: catalytic mechanism of 6-aminohexanoate-dimer hydrolase., Negoro S, Ohki T, Shibata N, Sasa K, Hayashi H, Nakano H, Yasuhira K, Kato D, Takeo M, Higuchi Y, J Mol Biol. 2007 Jun 29;370(1):142-56. Epub 2007 Apr 24. PMID:17512009

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (74 Kb) [Save to disk] Biological Unit Coordinates (2dcf.pdb1.gz) 70 Kb Biological Unit Coordinates (2dcf.pdb2.gz) 138 Kb LPC: Ligand-Protein Contacts for 2DCF CSU: Contacts of Structural Units for 2DCF Likely Quarternary Molecular Structure file(s) for 2DCF Structure Factors (1211 Kb) Retrieve 2DCF in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2DCF from S2C, [Save to disk] Re-refined 2dcf structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2DCF 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 2DCF

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 2DCF, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2dcf_A] [2dcf] SWISS-PROT database: [P07062] Domain organization of [NYLC_FLASK] by SWISSPFAM

Other resources with information on 2DCF

Community annotation for 2DCF at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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