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 FERREDOXIN-NADP REDUCTASE FROM SALMONELLA TYPHIMURIUM
 
Authors :  Y. Kim, M. Gu, J. Stam, W. F. Anderson, A. Joachimiak, Center For Struc Genomics Of Infectious Diseases (Csgid)
Date :  05 Jan 09  (Deposition) - 03 Feb 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Csgid, Alpha-Beta-Roll, Fad Binding Fold, Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Flavoprotein, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Kim, M. Gu, J. Stam, W. F. Anderson, A. Joachimiak
Crystal Structure Of Ferredoxin-Nadp Reductase From Salmonella Typhimurium
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - FERREDOXIN-NADP REDUCTASE
    Chains: A, B
    EC Number: 1.18.1.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21DE3-MAGIC
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: FPR, STM4084
    Organism Scientific: SALMONELLA TYPHIMURIUM
    Organism Taxid: 99287
    Strain: LT2

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3MG2Ligand/IonMAGNESIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:36 , ARG A:50 , ALA A:51 , TYR A:52 , SER A:53 , TYR A:66 , LEU A:67 , VAL A:68 , VAL A:70 , GLY A:73 , LYS A:74 , LEU A:75 , SER A:76 , THR A:116 , HIS A:246 , TYR A:247 , TRP A:248 , HOH A:271 , HOH A:422 , HOH A:452 , HOH A:480 , HOH A:601 , HOH A:607 , HOH A:609 , HOH A:643 , HOH A:654BINDING SITE FOR RESIDUE FAD A 301
2AC2SOFTWAREALA A:197 , HOH A:493 , HOH A:554 , HOH B:692BINDING SITE FOR RESIDUE MG A 249
3AC3SOFTWAREHOH A:555 , PHE B:36 , ARG B:50 , ALA B:51 , TYR B:52 , SER B:53 , TYR B:66 , LEU B:67 , VAL B:68 , VAL B:70 , GLY B:73 , LYS B:74 , LEU B:75 , SER B:76 , THR B:116 , TYR B:247 , TRP B:248 , HOH B:274 , HOH B:318 , HOH B:331 , HOH B:340 , HOH B:342 , HOH B:373 , HOH B:399 , HOH B:423 , HOH B:438 , HOH B:651BINDING SITE FOR RESIDUE FAD B 301
4AC4SOFTWAREHOH A:250 , HOH A:251 , HOH A:690 , ALA B:197 , HOH B:255 , HOH B:257 , HOH B:258BINDING SITE FOR RESIDUE MG B 249
5AC5SOFTWAREHOH A:261 , ASP B:101 , HOH B:259 , HOH B:381 , HOH B:491BINDING SITE FOR RESIDUE CA B 250

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3FPK)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3FPK)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3FPK)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3FPK)

(-) Exons   (0, 0)

(no "Exon" information available for 3FPK)

(-) 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:247
 aligned with Q8ZKP5_SALTY | Q8ZKP5 from UniProtKB/TrEMBL  Length:248

    Alignment length:247
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       
         Q8ZKP5_SALTY     2 ADWVTGKVTKVQNWTDALFSLTVHAPINPFTAGQFTKLGLEIDGERVQRAYSYVNAPDNPNLEFYLVTVPQGKLSPRLAALKPGDEVQVVSDASGFFVLDEVPDCETLWMLATGTAIGPYLSILQYGQDVARFKNLVLVHAARFAADLSYLPLMLELQQRYEGKLRIQTVVSRENVPGSLTGRVPALIENGELEKAVGLPMDKETSHVMLCGNPQMVRDTQQLLKETRQMTKHLRRRPGHMTAEHYW 248
               SCOP domains d3fpka1 A:2-100 automated matches                                                                  d3fpka2 A:101-248 automated matches                                                                                                                  SCOP domains
               CATH domains 3fpkA01 A:2-96 Translation factors                                                             3fpkA02 A:97-248 Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeee....eeeeeee..........eeeeeeee..eeeeeeee.........eeeeee......hhhhhhh.....eeeee.......hhhhh....eeeeeee...hhhhhhhhhhh.......eeeeeeee.hhhhh.hhhhhhhhhhhhh..eeeeeee........ee.hhhhhhhhhhhhhhhh.......eeeeeeehhhhhhhhhhhhhhhhh...........eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fpk A   2 ADWVTGKVTKVQNWTDALFSLTVHAPINPFTAGQFTKLGLEIDGERVQRAYSYVNAPDNPNLEFYLVTVPQGKLSPRLAALKPGDEVQVVSDASGFFVLDEVPDCETLWMLATGTAIGPYLSILQYGQDVARFKNLVLVHAARFAADLSYLPLMLELQQRYEGKLRIQTVVSRENVPGSLTGRVPALIENGELEKAVGLPMDKETSHVMLCGNPQMVRDTQQLLKETRQMTKHLRRRPGHMTAEHYW 248
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       


Chain B from PDB  Type:PROTEIN  Length:247
 aligned with Q8ZKP5_SALTY | Q8ZKP5 from UniProtKB/TrEMBL  Length:248

    Alignment length:247
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       
         Q8ZKP5_SALTY     2 ADWVTGKVTKVQNWTDALFSLTVHAPINPFTAGQFTKLGLEIDGERVQRAYSYVNAPDNPNLEFYLVTVPQGKLSPRLAALKPGDEVQVVSDASGFFVLDEVPDCETLWMLATGTAIGPYLSILQYGQDVARFKNLVLVHAARFAADLSYLPLMLELQQRYEGKLRIQTVVSRENVPGSLTGRVPALIENGELEKAVGLPMDKETSHVMLCGNPQMVRDTQQLLKETRQMTKHLRRRPGHMTAEHYW 248
               SCOP domains d3fpkb1 B:2-100 automated matches                                                                  d3fpkb2 B:101-248 automated matches                                                                                                                  SCOP domains
               CATH domains 3fpkB01 B:2-96 Translation factors                                                             3fpkB02 B:97-248 Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeee....eeeeeee..........eeeeeeee..eeeeeeee.........eeeeee......hhhhhhh.....eeeee.......hhhhh....eeeeeee...hhhhhhhhhhh.......eeeeeeee.hhhhh.hhhhhhhhhhhh...eeeeeee........ee.hhhhhhhhhhhhhhhh.......eeeeeeehhhhhhhhhhhhhhhhh...........eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fpk B   2 ADWVTGKVTKVQNWTDALFSLTVHAPINPFTAGQFTKLGLEIDGERVQRAYSYVNAPDNPNLEFYLVTVPQGKLSPRLAALKPGDEVQVVSDASGFFVLDEVPDCETLWMLATGTAIGPYLSILQYGQDVARFKNLVLVHAARFAADLSYLPLMLELQQRYEGKLRIQTVVSRENVPGSLTGRVPALIENGELEKAVGLPMDKETSHVMLCGNPQMVRDTQQLLKETRQMTKHLRRRPGHMTAEHYW 248
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241
   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)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3FPK)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q8ZKP5_SALTY | Q8ZKP5)
molecular function
    GO:0004324    ferredoxin-NADP+ reductase activity    Catalysis of the reaction: reduced ferredoxin + NADP+ = oxidized ferredoxin + NADPH + H+.
    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: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.

 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
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FAD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3fpk)
 

(-) 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
  3fpk
    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
  Q8ZKP5_SALTY | Q8ZKP5
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  1.18.1.2
    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
  Q8ZKP5_SALTY | Q8ZKP5
    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 3FPK)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3FPK)