1ZPD	Alcohol Fermentation	date	Apr 17, 1998
title	Pyruvate Decarboxylase From Zymomonas Mobilis
authors	G.Lu, D.Dobritzsch, G.Schneider
compound		source
Molecule: Pyruvate Decarboxylase Chain: A, B, E, F Ec: 4.1.1.1 Engineered: Yes		Organism_scientific: Zymomonas Mobilis Organism_taxid: 542 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Sg13009prep4 Expression_system_collection: Atcc 29191
symmetry	Space Group: P 1	R_factor 0.162 R_Free 0.197
crystal cell	length a length b length c angle alpha angle beta angle gamma 69.868 92.168 98.256 102.86 94.59 112.69
method	X-Ray Diffraction	resolution	1.86 Å
ligand	CIT, DPX, MG	enzyme	Lyase E.C.4.1.1.1 BRENDA
Gene Ontology	Chain Function Process Component F, A, E, B
Primary reference	High resolution crystal structure of pyruvate decarboxylase from Zymomonas mobilis. Implications for substrate activation in pyruvate decarboxylases., Dobritzsch D, Konig S, Schneider G, Lu G, J Biol Chem 1998 Aug 7;273(32):20196-204. PMID:9685367

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (390 Kb) [Save to disk] Biological Unit Coordinates (1zpd.pdb1.gz) 383 Kb LPC: Ligand-Protein Contacts for 1ZPD CSU: Contacts of Structural Units for 1ZPD Likely Quarternary Molecular Structure file(s) for 1ZPD Structure Factors (1679 Kb) Retrieve 1ZPD in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1ZPD from S2C, [Save to disk] Re-refined 1zpd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1ZPD 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 1ZPD

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 1ZPD, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1zpda1, region A:188-362 [Jmol] [rasmolscript] [script source]     - Domain d1zpda2, region A:2-187 [Jmol] [rasmolscript] [script source]     - Domain d1zpda3, region A:363-566 [Jmol] [rasmolscript] [script source]     - Domain d1zpdb1, region B:188-362 [Jmol] [rasmolscript] [script source]     - Domain d1zpdb2, region B:2-187 [Jmol] [rasmolscript] [script source]     - Domain d1zpdb3, region B:363-566 [Jmol] [rasmolscript] [script source]     - Domain d1zpde1, region E:188-362 [Jmol] [rasmolscript] [script source]     - Domain d1zpde2, region E:2-187 [Jmol] [rasmolscript] [script source]     - Domain d1zpde3, region E:363-566 [Jmol] [rasmolscript] [script source]     - Domain d1zpdf1, region F:188-362 [Jmol] [rasmolscript] [script source]     - Domain d1zpdf2, region F:2-187 [Jmol] [rasmolscript] [script source]     - Domain d1zpdf3, region F:363-566 [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: [1zpd_A] [1zpd_E] [1zpd] [1zpd_B] [1zpd_F] SWISS-PROT database: [P06672] Domain organization of [PDC_ZYMMO] by SWISSPFAM

Other resources with information on 1ZPD

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

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