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

(-) Description

Title :  CRYSTAL STRUCTURE OF ESCHERICHIA COLI QUINONE OXIDOREDUCTASE COMPLEXED WITH NADPH
 
Authors :  J. M. Thorn, J. D. Barton, N. E. Dixon, D. L. Ollis, K. J. Edwards
Date :  14 Feb 95  (Deposition) - 03 Jun 95  (Release) - 04 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. M. Thorn, J. D. Barton, N. E. Dixon, D. L. Ollis, K. J. Edwards
Crystal Structure Of Escherichia Coli Qor Quinone Oxidoreductase Complexed With Nadph.
J. Mol. Biol. V. 249 785 1995
PubMed-ID: 7602590  |  Reference-DOI: 10.1006/JMBI.1995.0337
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - QUINONE OXIDOREDUCTASE
    Cell Line: 293
    Chains: A, B
    Engineered: YES
    Expression System Strain: 293
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1NDP2Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
2SO42Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:43 , TYR A:46 , TYR A:52 , PHE A:238 , ASN A:240 , ARG A:263 , NDP A:350 , HOH A:373 , HOH A:481 , HOH B:482BINDING SITE FOR RESIDUE SO4 A 328
2AC2SOFTWAREILE B:43 , TYR B:46 , TYR B:52 , ARG B:263 , NDP B:350 , HOH B:355 , HOH B:380BINDING SITE FOR RESIDUE SO4 B 328
3AC3SOFTWAREPHE A:42 , TYR A:46 , THR A:127 , TYR A:130 , GLY A:151 , GLY A:152 , VAL A:153 , VAL A:172 , GLY A:173 , LYS A:177 , TYR A:192 , SER A:216 , PHE A:238 , GLY A:239 , ASN A:240 , SER A:241 , SER A:242 , ARG A:263 , PRO A:264 , SER A:265 , LEU A:266 , ARG A:317 , SO4 A:328 , HOH A:371 , HOH A:373 , HOH A:403 , HOH A:404 , HOH A:405 , HOH A:413 , HOH A:447 , HOH A:448 , HOH A:466 , HOH A:468 , HOH A:478 , HOH A:480BINDING SITE FOR RESIDUE NDP A 350
4AC4SOFTWAREPHE B:42 , TYR B:46 , LEU B:123 , THR B:127 , TYR B:130 , GLY B:151 , GLY B:152 , VAL B:153 , VAL B:172 , GLY B:173 , LYS B:177 , TYR B:192 , SER B:216 , PHE B:238 , GLY B:239 , ASN B:240 , SER B:241 , SER B:242 , ARG B:263 , PRO B:264 , SER B:265 , LEU B:266 , ARG B:317 , SO4 B:328 , HOH B:360 , HOH B:365 , HOH B:366 , HOH B:367 , HOH B:377 , HOH B:379 , HOH B:418 , HOH B:422 , HOH B:450 , HOH B:451 , HOH B:463 , HOH B:494 , HOH B:519BINDING SITE FOR RESIDUE NDP B 350

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1QOR)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Leu A:57 -Pro A:58
2Leu B:57 -Pro B:58

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1QOR)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1QOR_ZETA_CRYSTALPS01162 Quinone oxidoreductase / zeta-crystallin signature.QOR1_ECOLI141-162
 		  2A:141-162
B:141-162

(-) Exons   (0, 0)

(no "Exon" information available for 1QOR)

(-) Sequences/Alignments

Asymmetric/Biological 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:326
 aligned with QOR1_ECOLI | P28304 from UniProtKB/Swiss-Prot  Length:327

    Alignment length:326
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321      
           QOR1_ECOLI     2 ATRIEFHKHGGPEVLQAVEFTPADPAENEIQVENKAIGINFIDTYIRSGLYPPPSLPSGLGTEAAGIVSKVGSGVKHIKAGDRVVYAQSALGAYSSVHNIIADKAAILPAAISFEQAAASFLKGLTVYYLLRKTYEIKPDEQFLFHAAAGGVGLIACQWAKALGAKLIGTVGTAQKAQSALKAGAWQVINYREEDLVERLKEITGGKKVRVVYDSVGRDTWERSLDCLQRRGLMVSFGNSSGAVTGVNLGILNQKGSLYVTRPSLQGYITTREELTEASNELFSLIASGVIKVDVAEQQKYPLKDAQRAHEILESRATQGSSLLIP 327
               SCOP domains d1qora1 A:2-112,A:292-327 Quinone oxidoreductase                                                               d1qora2 A:113-291 Quinone oxidoreductase                                                                                                                                           d1qora1 A:2-112,A:292-327            SCOP domains
               CATH domains 1qorA01 A:2-123,A:270-327 Medium-chain alcohol dehydrogenases, catalytic domain                                           1qorA02 A:124-269 NAD(P)-binding Rossmann-like Domain                                                                                             1qorA01 A:2-123,A:270-327                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..........eeee.........eeeeeeeeee...hhhhhhh...............eeeeeeee...........eeeeeeeee.....eeeee...eee......hhhhhhhhhhhhhhhhhhh.........eeee.....hhhhhhhhhhhhh..eeeeee..hhhhhhhhhh...eeee.....hhhhhhhh.....eeeeee......hhhhhh.eeeeeeeee.............hhhhh....eee...hhhh...hhhhhhhhhhhhhhhh............eee...hhhhhhhhh........eee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------QOR_ZETA_CRYSTAL      --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qor A   2 ATRIEFHKHGGPEVLQAVEFTPADPAENEIQVENKAIGINFIDTYIRSGLYPPPSLPSGLGTEAAGIVSKVGSGVKHIKAGDRVVYAQSALGAYSSVHNIIADKAAILPAAISFEQAAASFLKGLTVYYLLRKTYEIKPDEQFLFHAAAGGVGLIACQWAKALGAKLIGTVGTAQKAQSALKAGAWQVINYREEDLVERLKEITGGKKVRVVYDSVGRDTWERSLDCLQRRGLMVSFGNSSGAVTGVNLGILNQKGSLYVTRPSLQGYITTREELTEASNELFSLIASGVIKVDVAEQQKYPLKDAQRAHEILESRATQGSSLLIP 327
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321      


Chain B from PDB  Type:PROTEIN  Length:326
 aligned with QOR1_ECOLI | P28304 from UniProtKB/Swiss-Prot  Length:327

    Alignment length:326
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321      
           QOR1_ECOLI     2 ATRIEFHKHGGPEVLQAVEFTPADPAENEIQVENKAIGINFIDTYIRSGLYPPPSLPSGLGTEAAGIVSKVGSGVKHIKAGDRVVYAQSALGAYSSVHNIIADKAAILPAAISFEQAAASFLKGLTVYYLLRKTYEIKPDEQFLFHAAAGGVGLIACQWAKALGAKLIGTVGTAQKAQSALKAGAWQVINYREEDLVERLKEITGGKKVRVVYDSVGRDTWERSLDCLQRRGLMVSFGNSSGAVTGVNLGILNQKGSLYVTRPSLQGYITTREELTEASNELFSLIASGVIKVDVAEQQKYPLKDAQRAHEILESRATQGSSLLIP 327
               SCOP domains d1qorb1 B:2-112,B:292-327 Quinone oxidoreductase                                                               d1qorb2 B:113-291 Quinone oxidoreductase                                                                                                                                           d1qorb1 B:2-112,B:292-327            SCOP domains
               CATH domains 1qorB01 B:2-123,B:270-327 Medium-chain alcohol dehydrogenases, catalytic domain                                           1qorB02 B:124-269 NAD(P)-binding Rossmann-like Domain                                                                                             1qorB01 B:2-123,B:270-327                                  CATH domains
           Pfam domains (1) --------------------------ADH_N-1qorB01 B:28-97                                                 ------------------------------------------------------ADH_zinc_N-1qorB03 B:152-285                                                                                                          ------------------------------------------ Pfam domains (1)
           Pfam domains (2) --------------------------ADH_N-1qorB02 B:28-97                                                 ------------------------------------------------------ADH_zinc_N-1qorB04 B:152-285                                                                                                          ------------------------------------------ Pfam domains (2)
         Sec.struct. author .eeee..........eeee.........eeeeeeeeee...hhhhhhh...............eeeeeeee...........eeeeeeeee.....eeeee...eee......hhhhhhhhhhhhhhhhhhh.........eeee.....hhhhhhhhhhhhh..eeeeee..hhhhhhhhhh...eeee.....hhhhhhhh.....eeeeee......hhhhhh.eeeeeeeee.............hhhhh....eee...hhhh...hhhhhhhhhhhhhhhh............eee...hhhhhhhhh........eee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------QOR_ZETA_CRYSTAL      --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qor B   2 ATRIEFHKHGGPEVLQAVEFTPADPAENEIQVENKAIGINFIDTYIRSGLYPPPSLPSGLGTEAAGIVSKVGSGVKHIKAGDRVVYAQSALGAYSSVHNIIADKAAILPAAISFEQAAASFLKGLTVYYLLRKTYEIKPDEQFLFHAAAGGVGLIACQWAKALGAKLIGTVGTAQKAQSALKAGAWQVINYREEDLVERLKEITGGKKVRVVYDSVGRDTWERSLDCLQRRGLMVSFGNSSGAVTGVNLGILNQKGSLYVTRPSLQGYITTREELTEASNELFSLIASGVIKVDVAEQQKYPLKDAQRAHEILESRATQGSSLLIP 327
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321
   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  (2, 4)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: GroES (70)
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (QOR1_ECOLI | P28304)
molecular function
    GO:0003960    NADPH:quinone reductase activity    Catalysis of the reaction: NADPH + H+ + quinone = NADP+ + semiquinone.
    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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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/Biological 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
    NDP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Leu A:57 - Pro A:58   [ RasMol ]  
    Leu B:57 - Pro B:58   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites 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
  1qor
    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
  QOR1_ECOLI | P28304
    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)
  (no 'Enzyme Classificator' available)
    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
  QOR1_ECOLI | P28304
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 1QOR)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1QOR)