2VK1	Lyase	date	Dec 16, 2007
title	Crystal Structure Of The Saccharomyces Cerevisiae Pyruvate Decarboxylase Variant D28a In Complex With Its Substrate
authors	S.Kutter, M.Weik, M.S.Weiss, S.Konig
compound		source
Molecule: Pyruvate Decarboxylase Isozyme 1 Chain: A, B, C, D Synonym: Pyruvate Decarboxylase Ec: 4.1.1.1 Engineered: Yes Mutation: Yes		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Yeast Organism_taxid: 4932 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Jm 109 Expression_system_plasmid: Puc 18
symmetry	Space Group: P 1 21 1	R_factor 0.191 R_Free 0.220
crystal cell	length a length b length c angle alpha angle beta angle gamma 80.880 141.310 114.410 90.00 107.19 90.00
method	X-Ray Diffraction	resolution	1.71 Å
ligand	MG, PYR, TPP	enzyme	Lyase E.C.4.1.1.1 BRENDA
Gene Ontology	Chain Function Process Component A, D, C, B
Primary reference	Covalently bound substrate at the regulatory site of yeast pyruvate decarboxylases triggers allosteric enzyme activation., Kutter S, Weiss MS, Wille G, Golbik R, Spinka M, Konig S, J Biol Chem. 2009 Feb 26. PMID:19246454

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (377 Kb) [Save to disk] Biological Unit Coordinates (2vk1.pdb1.gz) 189 Kb Biological Unit Coordinates (2vk1.pdb2.gz) 188 Kb LPC: Ligand-Protein Contacts for 2VK1 CSU: Contacts of Structural Units for 2VK1 Likely Quarternary Molecular Structure file(s) for 2VK1 Structure Factors (7975 Kb) Retrieve 2VK1 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2VK1 from S2C, [Save to disk] Re-refined 2vk1 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2VK1 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 2VK1

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 2VK1, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2vk1_C] [2vk1_A] [2vk1] [2vk1_B] [2vk1_D] SWISS-PROT database: [P06169] Domain organization of [PDC1_YEAST] by SWISSPFAM

Other resources with information on 2VK1

Community annotation for 2VK1 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

Movements, Movies and Images

Images from IMB Jena Image Library of Biological Macromolecules.

You may enter another PDB ID code

Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]

---

OCA© by Jaime Prilusky, 1996-2014,2022 Bioinformatics Unit Weizmann Institute of Science

---