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 Diffraction	resolution	1.75 Å
ligand	FAD	enzyme	Oxidoreductase E.C.1.6.2.2 BRENDA
related structures	by homologous chain: 1QX4
Gene Ontology	Chain Function Process Component A cytochrome-b5 reductase acti... AMP binding oxidoreductase activity ADP binding flavin adenine dinucleotide ... NAD binding lipid metabolic process steroid biosynthetic process... cholesterol biosynthetic pro... vitamin metabolic process water-soluble vitamin metabo... blood circulation steroid metabolic process cholesterol metabolic proces... sterol biosynthetic process L-ascorbic acid metabolic pr... small molecule metabolic pro... oxidation-reduction process cytoplasm mitochondrion mitochondrial outer membrane... mitochondrial inner membrane... endoplasmic reticulum endoplasmic reticulum membra... lipid particle hemoglobin complex membrane
Primary reference	Structure 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 (240 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. On AstexViewer, from MSD-EBI (viewer documentation). On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

Visual 3D analysis of 1UMK

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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_A] SWISS-PROT database: [P00387] Domain organization of [NB5R3_HUMAN] by SWISSPFAM Alignments of the sequence of 1UMK with the sequences similar proteins can be viewed for 1UMK's classification [NB5R3_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 [NB5R3_HUMAN] at ProtoMap. Click on the Cluster number.

Other resources with information on 1UMK

Community annotation for 1UMK at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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