Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF A NEW TYPE OF NADPH-DEPENDENT QUINONE OXIDOREDUCTASE (QOR2) FROM ESCHERICHIA COLI
 
Authors :  I. K. Kim, H. S. Yim, M. K. Kim, D. W. Kim, Y. M. Kim, S. S. Cha, S. O. Kang
Date :  13 Nov 07  (Deposition) - 27 May 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Alpha-Beta Sandwich, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. K. Kim, H. S. Yim, M. K. Kim, D. W. Kim, Y. M. Kim, S. S. Cha, S. O. Kang
Crystal Structure Of A New Type Of Nadph-Dependent Quinone Oxidoreductase (Qor2) From Escherichia Coli
J. Mol. Biol. V. 379 372 2008
PubMed-ID: 18455185  |  Reference-DOI: 10.1016/J.JMB.2008.04.003
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UNCHARACTERIZED OXIDOREDUCTASE YTFG
    Chains: A
    EC Number: 1.6.5.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Organism Scientific: ESCHERICHIA COLI
    Strain: STRAIN K12
    Synonym: HYPOTHETICAL PROTEIN YTFG, YTFG GENE PRODUCT, NADPH-DEPENDENT QUINONE OXIDOREDUCTASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1CU1Ligand/IonCOPPER (II) ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CU-1Ligand/IonCOPPER (II) ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CU-1Ligand/IonCOPPER (II) ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:13 , GLU A:17 , GLU A:276 , HIS A:280 , HOH A:1226BINDING SITE FOR RESIDUE CU A 1001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2ZCU)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2ZCU)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2ZCU)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2ZCU)

(-) Exons   (0, 0)

(no "Exon" information available for 2ZCU)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:275
 aligned with QOR2_ECOLI | P39315 from UniProtKB/Swiss-Prot  Length:286

    Alignment length:283
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280   
           QOR2_ECOLI     1 MIAITGATGQLGHYVIESLMKTVPASQIVAIVRNPAKAQALAAQGITVRQADYGDEAALTSALQGVEKLLLISSSEVGQRAPQHRNVINAAKAAGVKFIAYTSLLHADTSPLGLADEHIETEKMLADSGIVYTLLRNGWYSENYLASAPAALEHGVFIGAAGDGKIASATRADYAAAAARVISEAGHEGKVYELAGDSAWTLTQLAAELTKQSGKQVTYQNLSEADFAAALKSVGLPDGLADMLADSDVGASKGGLFDDSKTLSKLIGHPTTTLAESVSHLFN 283
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -NmrA-2zcuA01 A:2-221                                                                                                                                                                                                        -------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...hhhhhhhhhhhh...hhh.eeeee.....hhhhhhh..eeee....hhhhhhhhh....eeee..--------hhhhhhhhhhhhhh..eeeeeee.........hhhhhhhhhhhhhhhh.eeeeeee..hhhhhhhhhhhhhhhheeee..........hhhhhhhhhhhhhhh......eeee......hhhhhhhhhhhhhh...eeee.hhhhhhhhhh....hhhhhhhhhhhhhhhhh.......hhhhhhhh....hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zcu A   1 MIAITGATGQLGHYVIESLMKTVPASQIVAIVRNPAKAQALAAQGITVRQADYGDEAALTSALQGVEKLLLIS--------PQHRNVINAAKAAGVKFIAYTSLLHADTSPLGLADEHIETEKMLADSGIVYTLLRNGWYSENYLASAPAALEHGVFIGAAGDGKIASATRADYAAAAARVISEAGHEGKVYELAGDSAWTLTQLAAELTKQSGKQVTYQNLSEADFAAALKSVGLPDGLADMLADSDVGASKGGLFDDSKTLSKLIGHPTTTLAESVSHLFN 283
                                    10        20        30        40        50        60        70  |      - |      90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280   
                                                                                                   73       82
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 2ZCU)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2ZCU)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A   (QOR2_ECOLI | P39315)
molecular function
    GO:0003955    NAD(P)H dehydrogenase (quinone) activity    Catalysis of the reaction: NAD(P)H + H+ + a quinone = NAD(P)+ + a hydroquinone.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0016655    oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which NADH or NADPH acts as a hydrogen or electron donor and reduces a quinone or a similar acceptor molecule.
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    CU  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2zcu)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2zcu
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  QOR2_ECOLI | P39315
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  1.6.5.5
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  QOR2_ECOLI | P39315
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        QOR2_ECOLI | P39315: 2zcv

(-) Related Entries Specified in the PDB File

2zcv