1NI4 Oxidoreductase date Dec 20, 2002
title Human Pyruvate Dehydrogenase
authors E.Ciszak, L.G.Korotchkina, P.M.Dominiak, S.Sidhu, M.S.Patel
compound source
Molecule: Pyruvate Dehydrogenase E1 Component: Alpha Subunit;
Chain: A, C
Synonym: Pdhe1-A Type I
Ec: 1.2.4.1
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Dl41
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pqe-9

Molecule: Pyruvate Dehydrogenase E1 Component: Beta Subunit;
Chain: B, D
Synonym: Pdhe1-B
Ec: 1.2.4.1
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Dl41
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pqe-9
symmetry Space Group: P 21 21 21
R_factor 0.202 R_Free 0.244
crystal
cell
length a length b length c angle alpha angle beta angle gamma
64.337 126.889 190.638 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.95 Å
ligand K, MG, MSE, TPP enzyme Oxidoreductase E.C.1.2.4.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, C


D, B


Primary referenceStructural basis for flip-flop action of thiamin pyrophosphate-dependent enzymes revealed by human pyruvate dehydrogenase., Ciszak EM, Korotchkina LG, Dominiak PM, Sidhu S, Patel MS, J Biol Chem 2003 Jun 6;278(23):21240-6. PMID:12651851
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (244 Kb) [Save to disk]
  • Biological Unit Coordinates (1ni4.pdb1.gz) 234 Kb
  • LPC: Ligand-Protein Contacts for 1NI4
  • CSU: Contacts of Structural Units for 1NI4
  • Likely Quarternary Molecular Structure file(s) for 1NI4
  • Structure Factors (2970 Kb)
  • Retrieve 1NI4 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1NI4 from S2C, [Save to disk]
  • Re-refined 1ni4 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1NI4 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 1NI4
  • 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 1NI4, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1ni4a_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1ni4b1, region B:0-191 [Jmol] [rasmolscript] [script source]
        - Domain d1ni4b2, region B:192-329 [Jmol] [rasmolscript] [script source]
        - Domain d1ni4c_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1ni4d1, region D:0-191 [Jmol] [rasmolscript] [script source]
        - Domain d1ni4d2, region D:192-329 [Jmol] [rasmolscript] [script source]
  • Fold representative 1ni4 from FSSP and Dali (Families of Structurally Similar Proteins)
  • 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: [1ni4_C] [1ni4_B] [1ni4_D] [1ni4_A] [1ni4]
  • SWISS-PROT database: [P08559] [P11177]
  • Domain organization of [ODPA_HUMAN] [ODPB_HUMAN] by SWISSPFAM
  • Domain found in 1NI4: [Transket_pyr ] by SMART
  • Alignments of the sequence of 1NI4 with the sequences similar proteins can be viewed for 1NI4's classification [ODPA_HUMAN] [ODPB_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 [ODPA_HUMAN] [ODPB_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 1NI4
  • Community annotation for 1NI4 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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