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

(-) Description

Title :  CRYSTAL STRUCTURE OF FERREDOXIN REDUCTASE BPHA4 (HYDROQUINONE)
 
Authors :  T. Senda, M. Senda
Date :  12 Apr 07  (Deposition) - 16 Oct 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Flavoprotein, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Senda, S. Kishigami, S. Kimura, M. Fukuda, T. Ishida, T. Senda
Molecular Mechanism Of The Redox-Dependent Interaction Between Nadh-Dependent Ferredoxin Reductase And Rieske-Type [2Fe-2S] Ferredoxin
J. Mol. Biol. V. 373 382 2007
PubMed-ID: 17850818  |  Reference-DOI: 10.1016/J.JMB.2007.08.002

(-) Compounds

Molecule 1 - FERREDOXIN REDUCTASE
    ChainsA
    EC Number1.18.1.2
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneBPHA4
    Organism ScientificPSEUDOMONAS SP.
    Organism Taxid306
    StrainSTRAIN KKS102
    SynonymFERREDOXIN REDUCTASE BPHA4

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric Unit (3, 7)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2FMT5Ligand/IonFORMIC ACID
3NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Biological Unit 1 (3, 14)
No.NameCountTypeFull Name
1FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2FMT10Ligand/IonFORMIC ACID
3NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:14 , GLY A:16 , LEU A:17 , ALA A:18 , VAL A:38 , ASP A:40 , GLU A:41 , ARG A:48 , PRO A:49 , VAL A:80 , ALA A:82 , ALA A:108 , THR A:109 , GLY A:110 , LEU A:129 , ARG A:130 , ILE A:156 , GLU A:159 , GLY A:272 , ASP A:273 , GLU A:289 , THR A:290 , TRP A:291 , ALA A:294 , TYR A:319 , TRP A:320 , NAD A:1500 , HOH A:2006 , HOH A:2007 , HOH A:2008 , HOH A:2009 , HOH A:2012 , HOH A:2015 , HOH A:2034 , HOH A:2041 , HOH A:2043 , HOH A:2164BINDING SITE FOR RESIDUE FAD A 1449
2AC2SOFTWAREARG A:114 , LEU A:116 , ARG A:130 , VAL A:151 , GLY A:152 , GLY A:154 , VAL A:155 , ILE A:156 , GLU A:175 , THR A:176 , GLN A:177 , ARG A:183 , GLY A:234 , ILE A:235 , GLY A:236 , VAL A:237 , ASP A:273 , GLU A:289 , TYR A:319 , FAD A:1449 , HOH A:2087 , HOH A:2091 , HOH A:2117 , HOH A:2152 , HOH A:2159 , HOH A:2168 , HOH A:2189 , HOH A:2197BINDING SITE FOR RESIDUE NAD A 1500
3AC3SOFTWAREASP A:54 , HIS A:58 , GLY A:59 , ASP A:60 , ASP A:215BINDING SITE FOR RESIDUE FMT A 2001
4AC4SOFTWAREALA A:122 , THR A:123 , MET A:124 , SER A:213 , ASP A:215 , GLY A:216BINDING SITE FOR RESIDUE FMT A 2002
5AC5SOFTWAREARG A:327 , ASN A:369 , ASN A:370 , ALA A:371BINDING SITE FOR RESIDUE FMT A 2003
6AC6SOFTWAREVAL A:217 , ARG A:225 , TRP A:320 , ASP A:322BINDING SITE FOR RESIDUE FMT A 2004
7AC7SOFTWAREALA A:115 , LEU A:116 , VAL A:126BINDING SITE FOR RESIDUE FMT A 2005

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ala A:8 -Pro A:9

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2YVF)

(-) 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:401
 aligned with Q52437_PSES1 | Q52437 from UniProtKB/TrEMBL  Length:408

    Alignment length:401
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405 
         Q52437_PSES1     6 LKAPVVVLGAGLASVSFVAELRQAGYQGLITVVGDEAERPYDRPPLSKDFMAHGDAEKIRLDCKRAPEVEWLLGVTAQSFDPQAHTVALSDGRTLPYGTLVLATGAAPRALPTLQGATMPVHTLRTLEDARRIQAGLRPQSRLLIVGGGVIGLELAATARTAGVHVSLVETQPRLMSRAAPATLADFVARYHAAQGVDLRFERSVTGSVDGVVLLDDGTRIAADMVVVGIGVLANDALARAAGLACDDGIFVDAYGRTTCPDVYALGDVTRQRNPLSGRFERIETWSNAQNQGIAVARHLVDPTAPGYAELPWYWSDQGALRIQVAGLASGDEEIVRGEVSLDAPKFTLIELQKGRIVGATCVNNARDFAPLRRLLAVGAKPDRAALADPATDLRKLAAAV 406
               SCOP domains d2yvfa1 A:6-115,A:237-308 NADH-dependent ferredoxin reductase, BphA4                                          d2yvfa2 A:116-236 NADH-dependent ferredoxin reductase, BphA4                                                             d2yvfa1 A:6-115,A:237-308 NADH-dependent ferredoxin reductase, BphA4    d2yvfa3 A:309-406 NADH-dependent ferredoxin reductase, BphA4                                       SCOP domains
               CATH domains 2yvfA01 A:6-110,A:239-317  [code=3.50.50.60, no name defined]                                            ---2yvfA02 A:114-236  [code=3.50.50.60, no name defined]                                                                      --2yvfA01 A:6-110,A:239-317  [code=3.50.50.60, no name defined]                  2yvfA03 A:318-406  [code=3.30.390.30, no name defined]                                    CATH domains
           Pfam domains (1) ---------------------------------------------------------------------------------------------------------------------------------------------Pyr_redox-2yvfA01 A:147-223                                                  --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ---Pyr_redox_2-2yvfA02 A:9-279                                                                                                                                                                                                                                                    ------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ....eeee..hhhhhhhhhhhhhhh....eeeee........hhhhhhhhhhhhhhhhh..........eeee...eeeee....eeee....eee..eeee...eee..hhhhh.....eee..hhhhhhhhhh......eeeee..hhhhhhhhhhhhhh..eeeee...........hhhhhhhhhhhhhhh..eee....eeeee..eeee....eee..eeee...eee.hhhhhhhh......ee...........eee....eeeee....eeee..hhhhhhhhhhhhhhhhhh..........eeeeee..eeeeeee.....eeeee.........eeeeeee..eeeeeeee.hhhhhhhhhhhhhh....hhhhhhh...hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yvf A   6 LKAPVVVLGAGLASVSFVAELRQAGYQGLITVVGDEAERPYDRPPLSKDFMAHGDAEKIRLDCKRAPEVEWLLGVTAQSFDPQAHTVALSDGRTLPYGTLVLATGAAPRALPTLQGATMPVHTLRTLEDARRIQAGLRPQSRLLIVGGGVIGLELAATARTAGVHVSLVETQPRLMSRAAPATLADFVARYHAAQGVDLRFERSVTGSVDGVVLLDDGTRIAADMVVVGIGVLANDALARAAGLACDDGIFVDAYGRTTCPDVYALGDVTRQRNPLSGRFERIETWSNAQNQGIAVARHLVDPTAPGYAELPWYWSDQGALRIQVAGLASGDEEIVRGEVSLDAPKFTLIELQKGRIVGATCVNNARDFAPLRRLLAVGAKPDRAALADPATDLRKLAAAV 406
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405 

   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, 3)

Asymmetric Unit

(-) CATH Domains  (2, 3)

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

(-) Pfam Domains  (2, 2)

Asymmetric Unit

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q52437_PSES1 | Q52437)
molecular function
    GO:0050660    flavin adenine dinucleotide binding    Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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.
biological process
    GO:0045454    cell redox homeostasis    Any process that maintains the redox environment of a cell or compartment within a cell.
    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:0005623    cell    The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.

 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
    FAD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FMT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ala A:8 - Pro A:9   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2yvf
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  Q52437_PSES1 | Q52437
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  1.18.1.2
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  Q52437_PSES1 | Q52437
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q52437_PSES1 | Q524371d7y 1f3p 2gqw 2gr0 2gr1 2gr2 2gr3 2yvg 2yvj

(-) Related Entries Specified in the PDB File

2yvg