3CRK	Transferase	date	Apr 07, 2008
title	Crystal Structure Of The Pdhk2-L2 Complex.
authors	T.J.Green, K.M.Popov, M.Luo, A.Grigorian, A.Klyuyeva, A.Tuganova
compound		source
Molecule: Pyruvate Dehydrogenase [Lipoamide] Kinase Isozyme Mitochondrial; Chain: A, B Synonym: Pyruvate Dehydrogenase Kinase Isoform 2, Pdk P45 Ec: 2.7.11.2 Engineered: Yes		Organism_scientific: Rattus Norvegicus Organism_common: Norway Rat Organism_taxid: 10116 Gene: Pdk2 Expression_system: Escherichia Coli Bl21(De3) Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet28
Molecule: Dihydrolipoyllysine-Residue Acetyltransferase Com Pyruvate Dehydrogenase Complex, Mitochondrial; Chain: C, D Fragment: Unp Residues 181-267 Synonym: Pyruvate Dehydrogenase Complex E2 Subunit, Pdce2, Dihydrolipoamide S- Acetyltransferase Component Of Pyruvate Dehydrogenase Complex, Pdc- E2, 70 Kda Mitochondrial Autoan Primary Biliary Cirrhosis, Pbc, M2 Antigen Complex 70 Kda S Ec: 2.3.1.12 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Dlat, Dlta Expression_system: Escherichia Coli Bl21(De3) Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet28
symmetry	Space Group: P 1 21 1	R_factor 0.208 R_Free 0.251
crystal cell	length a length b length c angle alpha angle beta angle gamma 71.380 120.679 71.466 90.00 96.03 90.00
method	X-Ray Diffraction	resolution	2.30 Å
ligand	K, LA2	enzyme	Transferase E.C.2.7.11.2 BRENDA
Gene Ontology	Chain Function Process Component A, B nucleotide binding protein serine/threonine kin... pyruvate dehydrogenase (acet... ATP binding kinase activity transferase activity protein complex binding protein homodimerization act... protein heterodimerization a... carbohydrate metabolic proce... glucose metabolic process regulation of gluconeogenesi... protein phosphorylation regulation of pH insulin receptor signaling p... regulation of acetyl-CoA bio... regulation of cellular keton... regulation of glucose metabo... phosphorylation peptidyl-serine phosphorylat... cellular response to nutrien... glucose homeostasis mitochondrion mitochondrial matrix mitochondrial pyruvate dehyd... pyruvate dehydrogenase compl...
Primary reference	Structural and functional insights into the molecular mechanisms responsible for the regulation of pyruvate dehydrogenase kinase 2., Green T, Grigorian A, Klyuyeva A, Tuganova A, Luo M, Popov KM, J Biol Chem. 2008 Apr 3;. PMID:18387944

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (160 Kb) [Save to disk] Biological Unit Coordinates (3crk.pdb1.gz) 150 Kb LPC: Ligand-Protein Contacts for 3CRK CSU: Contacts of Structural Units for 3CRK Likely Quarternary Molecular Structure file(s) for 3CRK Structure Factors (385 Kb) Retrieve 3CRK in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3CRK from S2C, [Save to disk] Re-refined 3crk structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3CRK 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 3CRK

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 3CRK, from MSDmotif at EBI Fold representative 3crk from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3crk_A] [3crk_B] [3crk_C] [3crk_D] SWISS-PROT database: [P10515] [Q64536] Domain organization of [ODP2_HUMAN] [PDK2_RAT] by SWISSPFAM Domain found in 3CRK: [HATPase_c ] by SMART Alignments of the sequence of 3CRK with the sequences similar proteins can be viewed for 3CRK's classification [ODP2_HUMAN] [PDK2_RAT] 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 [ODP2_HUMAN] [PDK2_RAT] at ProtoMap. Click on the Cluster number.

Other resources with information on 3CRK

Community annotation for 3CRK at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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