1V1R Oxidoreductase date Apr 22, 2004
title Crosstalk Between Cofactor Binding And The Phosphorylation Loop Conformation In The Bckd Machine
authors J.Li, R.M.Wynn, M.Machius, J.L.Chuang, S.Karthikeyan, D.R.Tomchic D.T.Chuang
compound source
Molecule: 2-Oxoisovalerate Dehydrogenase Alpha Subunit
Chain: A
Synonym: Mitochondrial Precursor, Branched-Chain Alpha-Keto Dehydrogenase E1, Component Alpha Chain, Bckdh E1-Alpha, B
Ec: 1.2.4.4
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl-21 Cells With Overexpressing G Groes;
Expression_system_vector_type: Plasmid
Expression_system_vector: Ptrchisb (Invitrogen)
Expression_system_plasmid: Ptrc-Alpha-Betahis

Molecule: 2-Oxoisovalerate Dehydrogenase Beta Subunit
Chain: B
Synonym: Mitochondrial Precursor, Branched-Chain Alpha-Keto Dehydrogenase E1, Component Beta Chain, Bckdh E1-Beta;
Ec: 1.2.4.4
Engineered: Yes
Other_details: Apo-Form

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl-21 Cells With Overexpressing G Groes;
Expression_system_vector_type: Plasmid
Expression_system_vector: Ptrchisb (Invitrogen)
Expression_system_plasmid: Ptrc-Alpha-Betahis
Other_details: Expression System Used Bl-21 Cells With Overexpressing Groel And Groes
symmetry Space Group: P 31 2 1
R_factor 0.157 R_Free 0.183
crystal
cell
length a length b length c angle alpha angle beta angle gamma
145.135 145.135 69.226 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.8 Å
ligand CL, GOL, K, NA, SO4 enzyme Oxidoreductase E.C.1.2.4.4 BRENDA
related structures by homologous chain: 1U5B, 1X7W
Gene
Ontology
ChainFunctionProcessComponent
A


B


Primary referenceCross-talk between thiamin diphosphate binding and phosphorylation loop conformation in human branched-chain alpha-keto acid decarboxylase/dehydrogenase., Li J, Wynn RM, Machius M, Chuang JL, Karthikeyan S, Tomchick DR, Chuang DT, J Biol Chem. 2004 Jul 30;279(31):32968-78. Epub 2004 May 27. PMID:15166214
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (134 Kb) [Save to disk]
  • Biological Unit Coordinates (1v1r.pdb1.gz) 248 Kb
  • LPC: Ligand-Protein Contacts for 1V1R
  • CSU: Contacts of Structural Units for 1V1R
  • Likely Quarternary Molecular Structure file(s) for 1V1R
  • Structure Factors (1105 Kb)
  • Retrieve 1V1R in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1V1R from S2C, [Save to disk]
  • Re-refined 1v1r structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1V1R 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 1V1R
  • 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 1V1R, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1v1ra_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1v1rb1, region B:2-204 [Jmol] [rasmolscript] [script source]
        - Domain d1v1rb2, region B:205-342 [Jmol] [rasmolscript] [script source]
  • Fold representative 1v1r 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: [1v1r_B] [1v1r_A] [1v1r]
  • SWISS-PROT database: [P12694] [P21953]
  • Domain organization of [ODBA_HUMAN] [ODBB_HUMAN] by SWISSPFAM
  • Domain found in 1V1R: [Transket_pyr ] by SMART
  • Other resources with information on 1V1R
  • Community annotation for 1V1R 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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