2ZGC	Hydrolase	date	Jan 21, 2008
title	Crystal Structure Of Active Human Granzyme M
authors	L.F.Wu, L.Wang, G.Q.Hua, K.Liu, Y.J.Zhai, F.Sun, Z.S.Fan
compound		source
Molecule: Granzyme M Chain: A Synonym: Met-Ase, Natural Killer Cell Granular Protease, Hu Met-1 Serine Protease; Ec: 3.4.21.- Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Gzmm, Met1 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Rosetta(De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet26b-Gzmm
symmetry	Space Group: P 31 2 1	R_factor 0.209 R_Free 0.257
crystal cell	length a length b length c angle alpha angle beta angle gamma 74.391 74.391 113.199 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	1.96 Å
ligand	SO4	enzyme	Hydrolase E.C.3.4.21 BRENDA
Gene Ontology	Chain Function Process Component A endopeptidase activity peptidase activity serine-type peptidase activi... hydrolase activity proteolysis apoptotic process cytolysis innate immune response extracellular region
Primary reference	Structural basis for proteolytic specificity of the human apoptosis-inducing granzyme M., Wu L, Wang L, Hua G, Liu K, Yang X, Zhai Y, Bartlam M, Sun F, Fan Z, J Immunol. 2009 Jul 1;183(1):421-9. PMID:19542453

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (47 Kb) [Save to disk] Biological Unit Coordinates (2zgc.pdb1.gz) 42 Kb LPC: Ligand-Protein Contacts for 2ZGC CSU: Contacts of Structural Units for 2ZGC Likely Quarternary Molecular Structure file(s) for 2ZGC Structure Factors (145 Kb) Retrieve 2ZGC in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2ZGC from S2C, [Save to disk] Re-refined 2zgc structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2ZGC 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. On AstexViewer, from MSD-EBI (viewer documentation). On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

Visual 3D analysis of 2ZGC

Cartoon representation from PDB Cartoon 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 Crystal Contacts, from CryCo at Weizmann Institute 3D motif for 2ZGC, from MSDmotif at EBI Fold representative 2zgc from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2zgc_A] SWISS-PROT database: [P51124] Domain organization of [GRAM_HUMAN] by SWISSPFAM Domain found in 2ZGC: [Tryp_SPc ] by SMART Alignments of the sequence of 2ZGC with the sequences similar proteins can be viewed for 2ZGC's classification [GRAM_HUMAN] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list. A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [GRAM_HUMAN] at ProtoMap. Click on the Cluster number.

Other resources with information on 2ZGC

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

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