1JKD	Lysozyme	date	Nov 13, 1996
title	Human Lysozyme Mutant With Trp 109 Replaced By Ala
authors	M.Muraki, K.Harata, S.Goda, H.Nagahora
compound		source
Molecule: Lysozyme Chain: A Ec: 3.2.1.17 Engineered: Yes Mutation: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: A Synthetic Gene Of Human Lyso Expression_system: Saccharomyces Cerevisiae Expression_system_common: Baker'S Yeast Expression_system_taxid: 4932 Expression_system_strain: Ksc22-1c Expression_system_vector_type: Yep Expression_system_plasmid: Yephlysig (Ala109) Expression_system_gene: A Synthetic Gene Of Human Lysozyme Mutation Of W109a
symmetry	Space Group: P 21 21 21	R_factor 0.174 R_Free 0.245
crystal cell	length a length b length c angle alpha angle beta angle gamma 57.210 61.190 32.990 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	1.80 Å
ligand	NO3	enzyme	Hydrolase E.C.3.2.1.17 BRENDA
related structures	by homologous chain: 1LMN, 2BQI
Gene Ontology	Chain Function Process Component A
Primary reference	Importance of van der Waals contact between Glu 35 and Trp 109 to the catalytic action of human lysozyme., Muraki M, Goda S, Nagahora H, Harata K, Protein Sci 1997 Feb;6(2):473-6. PMID:9041653

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (26 Kb) [Save to disk] Biological Unit Coordinates (1jkd.pdb1.gz) 22 Kb LPC: Ligand-Protein Contacts for 1JKD CSU: Contacts of Structural Units for 1JKD Likely Quarternary Molecular Structure file(s) for 1JKD Structure Factors (112 Kb) Retrieve 1JKD in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1JKD from S2C, [Save to disk] Re-refined 1jkd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1JKD 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 1JKD

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 1JKD, from MSDmotif at EBI Genome occurence of 1JKD's fold from GeneCensus Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1jkd__, region [Jmol] [rasmolscript] [script source] Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH Summaries and structural analyses of PDB data files from PDBSum Identification of Protein Pockets & Cavities at CASTp

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1jkd] [1jkd_A] SWISS-PROT database: [P61626] Domain organization of [LYSC_HUMAN] by SWISSPFAM Domain found in 1JKD: [LYZ1 ] by SMART

Other resources with information on 1JKD

Community annotation for 1JKD at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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