1Y8N Transferase date Dec 13, 2004
title Crystal Structure Of The Pdk3-L2 Complex
authors M.Kato, J.L.Chuang, R.M.Wynn, D.T.Chuang
compound source
Molecule: [Pyruvate Dehydrogenase [Lipoamide]] Kinase Isozy
Chain: A
Synonym: Pyruvate Dehydrogenase Kinase Isoform 3
Ec: 2.7.1.99
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pdk3
Expression_system: Escherichia Coli Bl21
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Ptrchisb

Molecule: Dihydrolipoyllysine-Residue Acetyltransferase Com Pyruvate Dehydrogenase Complex;
Chain: B
Synonym: E2, Dihydrolipoamide Acetyltransferase Component O Dehydrogenase Complex, Pdc-E2, 70 Kda Mitochondrial Autoant 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
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Ptrchisb
symmetry Space Group: P 65 2 2
R_factor 0.210 R_Free 0.248
crystal
cell
length a length b length c angle alpha angle beta angle gamma
120.806 120.806 238.587 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.60 Å
ligand K, LPA, RED enzyme Transferase E.C.2.7.1.99 BRENDA
related structures by homologous chain: 1JM6, 1Y8O, 1Y8P
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceCrystal structure of pyruvate dehydrogenase kinase 3 bound to lipoyl domain 2 of human pyruvate dehydrogenase complex., Kato M, Chuang JL, Tso SC, Wynn RM, Chuang DT, EMBO J 2005 May 18;24(10):1763-74. Epub 2005 Apr 28. PMID:15861126
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (85 Kb) [Save to disk]
  • Biological Unit Coordinates (1y8n.pdb1.gz) 156 Kb
  • LPC: Ligand-Protein Contacts for 1Y8N
  • CSU: Contacts of Structural Units for 1Y8N
  • Likely Quarternary Molecular Structure file(s) for 1Y8N
  • Structure Factors (434 Kb)
  • Retrieve 1Y8N in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1Y8N from S2C, [Save to disk]
  • Re-refined 1y8n structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1Y8N 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 1Y8N
  • 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 1Y8N, from MSDmotif at EBI
  • Fold representative 1y8n from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1y8n_A] [1y8n] [1y8n_B]
  • SWISS-PROT database: [P10515] [Q15120]
  • Domain organization of [ODP2_HUMAN] [PDK3_HUMAN] by SWISSPFAM
  • Domain found in 1Y8N: [HATPase_c ] by SMART
  • Other resources with information on 1Y8N
  • Community annotation for 1Y8N at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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