1UMK Oxidoreductase date Oct 03, 2003
title The Structure Of Human Erythrocyte Nadh-Cytochrome B5 Reductase
authors S.Bando, T.Takano, T.Yubisui, K.Shirabe, M.Takeshita, C.Horii, A.Nakagawa
compound source
Molecule: Nadh-Cytochrome B5 Reductase
Chain: A
Synonym: B5r
Ec: 1.6.2.2
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Puc13
symmetry Space Group: P 41
R_factor 0.165 R_Free 0.207
crystal
cell
length a length b length c angle alpha angle beta angle gamma
65.869 65.869 76.200 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.75 Å
ligand FAD enzyme Oxidoreductase E.C.1.6.2.2 BRENDA
related structures by homologous chain: 1QX4
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructure of human erythrocyte NADH-cytochrome b5 reductase., Bando S, Takano T, Yubisui T, Shirabe K, Takeshita M, Nakagawa A, Acta Crystallogr D Biol Crystallogr. 2004 Nov;60(Pt 11):1929-34. Epub 2004, Oct 20. PMID:15502298
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (65 Kb) [Save to disk]
  • Biological Unit Coordinates (1umk.pdb1.gz) 61 Kb
  • LPC: Ligand-Protein Contacts for 1UMK
  • CSU: Contacts of Structural Units for 1UMK
  • Likely Quarternary Molecular Structure file(s) for 1UMK
  • Structure Factors (233 Kb)
  • Retrieve 1UMK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1UMK from S2C, [Save to disk]
  • Re-refined 1umk structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1UMK 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 1UMK
  • 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 1UMK, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1umka2, region A:154-300 [Jmol] [rasmolscript] [script source]
        - Domain d1umka1, region A:30-153 [Jmol] [rasmolscript] [script source]
  • Fold representative 1umk 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: [1umk] [1umk_A]
  • SWISS-PROT database: [P00387]
  • Domain organization of [NB5R3_HUMAN] by SWISSPFAM
  • Other resources with information on 1UMK
  • Community annotation for 1UMK 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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