1NEN Oxidoreductase Electron Transport date Dec 11, 2002
title Complex II (Succinate Dehydrogenase) From E. Coli With Dinitrophenol-17 Inhibitor Co-Crystallized At The Ubiquinone Binding Site
authors V.Yankovskaya, R.Horsefield, S.Tornroth, C.Luna-Chavez, H.Miyoshi, C.Leger, B.Byrne, G.Cecchini, S.Iwata
compound source
Molecule: Succinate Dehydrogenase Flavoprotein Subunit
Chain: A
Ec: 1.3.99.1, 1.3.5.1
Engineered: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 562
Gene: Sdha Or B0723 Or Z0877 Or Ecs0748
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pfas

Molecule: Succinate Dehydrogenase Iron-Sulfur Protein
Chain: B
Ec: 1.3.99.1, 1.3.5.1
Engineered: Yes

Organism_scientific: Escherichia Coli
Organism_taxid: 562
Gene: Sdhb Or B0724
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pfas

Molecule: Succinate Dehydrogenase Cytochrome B-556 Subunit
Chain: C
Engineered: Yes

Organism_scientific: Escherichia Coli
Organism_taxid: 562
Gene: Sdhc Or Cyba Or B0721 Or Z0875 Or Ecs0746
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pfas

Molecule: Succinate Dehydrogenase Hydrophobic Membrane Anchor Protein;
Chain: D
Engineered: Yes

Organism_scientific: Escherichia Coli
Organism_taxid: 562
Gene: Sdhd Or B0722
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pfas
symmetry Space Group: H 3 2
R_factor 0.271 R_Free 0.296
crystal
cell
length a length b length c angle alpha angle beta angle gamma
138.800 138.800 521.900 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.90 Å
ligand CA, CDN, DNT, EPH, F3S, FAD, FES, HEM, OAA, SF4 enzyme Oxidoreductase E.C.1.3.99.1 BRENDA
related structures by homologous chain: 1NEK
Gene
Ontology
ChainFunctionProcessComponent
A


B


C
  • electron transfer activity


  • D
  • electron transfer activity


  • Primary referenceArchitecture of succinate dehydrogenase and reactive oxygen species generation., Yankovskaya V, Horsefield R, Tornroth S, Luna-Chavez C, Miyoshi H, Leger C, Byrne B, Cecchini G, Iwata S, Science 2003 Jan 31;299(5607):700-4. PMID:12560550
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (187 Kb) [Save to disk]
  • Biological Unit Coordinates (1nen.pdb1.gz) 179 Kb
  • Biological Unit Coordinates (1nen.pdb2.gz) 524 Kb
  • Biological Unit Coordinates (1nen.pdb3.gz) 352 Kb
  • LPC: Ligand-Protein Contacts for 1NEN
  • CSU: Contacts of Structural Units for 1NEN
  • Likely Quarternary Molecular Structure file(s) for 1NEN
  • Retrieve 1NEN in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1NEN from S2C, [Save to disk]
  • View 1NEN 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 1NEN
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1NEN, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1nena2, region A:1-235,A:356-450 [Jmol] [rasmolscript] [script source]
        - Domain d1nena3, region A:236-355 [Jmol] [rasmolscript] [script source]
        - Domain d1nena1, region A:451-588 [Jmol] [rasmolscript] [script source]
        - Domain d1nenb2, region B:1-106 [Jmol] [rasmolscript] [script source]
        - Domain d1nenb1, region B:107-238 [Jmol] [rasmolscript] [script source]
        - Domain d1nenc_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1nend_, region D [Jmol] [rasmolscript] [script source]
  • 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: [1nen] [1nen_B] [1nen_C] [1nen_A] [1nen_D]
  • SWISS-PROT database: [P0AC41] [P07014] [P69054] [P0AC44]
  • Domain organization of [DHSA_ECOLI] [DHSB_ECOLI] [DHSC_ECOLI] [DHSD_ECOLI] by SWISSPFAM
  • Other resources with information on 1NEN
  • Community annotation for 1NEN at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
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  • Images from IMB Jena Image Library of Biological Macromolecules.

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