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 :  FERREDOXIN-NADP REDUCTASE
 
Authors :  M. R. Sawaya, C. A. Kerfeld, C. Gomez-Lojero, D. Krogmann, D. A. Bryant, T. O. Yeates
Date :  29 Sep 05  (Deposition) - 11 Oct 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Complex With Fad, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. R. Sawaya, C. A. Kerfeld, C. Gomez-Lojero, D. Krogmann, D. A. Bryant T. O. Yeates
Crystal Structure Of Ferredoxin-Nadp Reductase From Synechococcus Sp. (Pcc 7002)
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - FERREDOXIN--NADP REDUCTASE
    Chains: A, B
    EC Number: 1.18.1.2
    Organism Scientific: SYNECHOCOCCUS SP. PCC 7002
    Organism Taxid: 32049
    Synonym: FNR

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 13)

Asymmetric Unit (2, 13)
No.NameCountTypeFull Name
1FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2SO411Ligand/IonSULFATE ION
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2SO45Ligand/IonSULFATE ION
Biological Unit 2 (2, 7)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2SO46Ligand/IonSULFATE ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN A:366 , ARG A:388 , LYS A:392 , TRP A:397BINDING SITE FOR RESIDUE SO4 A 407
02AC2SOFTWAREASP A:170 , HIS A:176 , LYS A:177 , ARG A:179 , LYS A:281BINDING SITE FOR RESIDUE SO4 A 408
03AC3SOFTWAREARG A:187 , HIS A:188 , ARG A:271 , HIS A:277BINDING SITE FOR RESIDUE SO4 A 409
04AC4SOFTWARETYR A:206 , GLN A:207 , FAD A:403 , HOH A:451 , TYR B:206 , FAD B:403BINDING SITE FOR RESIDUE SO4 A 410
05AC5SOFTWAREGLY A:240 , LYS A:241 , GLU A:242BINDING SITE FOR RESIDUE SO4 A 414
06AC6SOFTWAREHIS B:176 , LYS B:177 , ARG B:179BINDING SITE FOR RESIDUE SO4 B 405
07AC7SOFTWAREHIS B:188 , ARG B:271 , HIS B:277 , GLU B:278BINDING SITE FOR RESIDUE SO4 B 406
08AC8SOFTWAREGLN B:366 , ARG B:388 , LYS B:392 , TRP B:397 , VAL B:399BINDING SITE FOR RESIDUE SO4 B 411
09AC9SOFTWARELYS A:274 , LYS A:306 , LYS B:274 , LYS B:306BINDING SITE FOR RESIDUE SO4 B 412
10BC1SOFTWAREGLY B:240 , LYS B:241 , GLU B:242BINDING SITE FOR RESIDUE SO4 B 413
11BC2SOFTWARELYS A:393 , GLN B:325BINDING SITE FOR RESIDUE SO4 B 415
12BC3SOFTWAREARG A:179 , LEU A:180 , TYR A:181 , SER A:182 , CYS A:200 , VAL A:201 , ARG A:202 , LEU A:204 , TYR A:206 , GLY A:217 , VAL A:218 , CYS A:219 , SER A:220 , THR A:260 , GLU A:400 , TYR A:402 , SO4 A:410 , HOH A:419 , HOH A:431 , HOH A:435 , HOH A:441 , GLY B:381 , LEU B:382 , ASN B:383 , GLU B:386BINDING SITE FOR RESIDUE FAD A 403
13BC4SOFTWARESO4 A:410 , ARG B:179 , LEU B:180 , TYR B:181 , SER B:182 , CYS B:200 , ARG B:202 , LEU B:204 , TYR B:206 , GLY B:217 , VAL B:218 , CYS B:219 , SER B:220 , THR B:260 , ARG B:389 , LYS B:393 , GLU B:400 , TYR B:402 , HOH B:420 , HOH B:434 , HOH B:484BINDING SITE FOR RESIDUE FAD B 403

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2B5O)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2B5O)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2B5O)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FAD_FRPS51384 Ferredoxin reductase-type FAD binding domain profile.FENR_SYNP2120-245
 		  2A:120-245
B:120-245
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FAD_FRPS51384 Ferredoxin reductase-type FAD binding domain profile.FENR_SYNP2120-245
 		  1A:120-245
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FAD_FRPS51384 Ferredoxin reductase-type FAD binding domain profile.FENR_SYNP2120-245
 		  1-
B:120-245

(-) Exons   (0, 0)

(no "Exon" information available for 2B5O)

(-) 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:292
 aligned with FENR_SYNP2 | P31973 from UniProtKB/Swiss-Prot  Length:402

    Alignment length:292
                                   120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400  
           FENR_SYNP2   111 SVPVNIYRPKTPFLGKCIENYELVDEGGSGTVRHVTFDISEGDLRYLEGQSIGIIPPGEDKNGKPHKLRLYSIASTRHGDMEDNKTVSLCVRQLEYQDPESGETVYGVCSTYLCNLPVGTDDVKITGPVGKEMLLPDDEDATVVMLATGTGIAPFRAFLWRMFKEQHEDYKFKGKAWLIFGVPYTANILYKDDFEKMAAENPDNFRLTYAISREQKTADGGKVYVQSRVSEYADELFEMIQKPNTHVYMCGLKGMQPPIDETFTAEAEKRGLNWEEMRRSMKKEHRWHVEVY 402
               SCOP domains d2b5oa1 A:111-242 automated matches                                                                                                 d2b5oa2 A:243-402 automated matches                                                                                                                              SCOP domains
               CATH domains 2b5oA01 A:111-239 Translation factors                                                                                            2b5oA02 A:240-402 Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module                                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeeeeeeee.........eeeeeee............eeeee...ee...ee...eeee.............eeeeeee..eee......eeehhhhhhhhh.......eeeeeee............eeeeeee...hhhhhhhhhhhhh..........eeeeeeee.hhhhh.hhhhhhhhhhhh...eeeeeee............hhhhhhhhhhhhhhhhhh...eeeeeeehhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh..eeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------FAD_FR  PDB: A:120-245 UniProt: 120-245                                                                                       ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2b5o A 111 SVPVNIYRPKTPFLGKCIENYELVDEGGSGTVRHVTFDISEGDLRYLEGQSIGIIPPGEDKNGKPHKLRLYSIASTRHGDMEDNKTVSLCVRQLEYQDPESGETVYGVCSTYLCNLPVGTDDVKITGPVGKEMLLPDDEDATVVMLATGTGIAPFRAFLWRMFKEQHEDYKFKGKAWLIFGVPYTANILYKDDFEKMAAENPDNFRLTYAISREQKTADGGKVYVQSRVSEYADELFEMIQKPNTHVYMCGLKGMQPPIDETFTAEAEKRGLNWEEMRRSMKKEHRWHVEVY 402
                                   120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400  


Chain B from PDB  Type:PROTEIN  Length:292
 aligned with FENR_SYNP2 | P31973 from UniProtKB/Swiss-Prot  Length:402

    Alignment length:292
                                   120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400  
           FENR_SYNP2   111 SVPVNIYRPKTPFLGKCIENYELVDEGGSGTVRHVTFDISEGDLRYLEGQSIGIIPPGEDKNGKPHKLRLYSIASTRHGDMEDNKTVSLCVRQLEYQDPESGETVYGVCSTYLCNLPVGTDDVKITGPVGKEMLLPDDEDATVVMLATGTGIAPFRAFLWRMFKEQHEDYKFKGKAWLIFGVPYTANILYKDDFEKMAAENPDNFRLTYAISREQKTADGGKVYVQSRVSEYADELFEMIQKPNTHVYMCGLKGMQPPIDETFTAEAEKRGLNWEEMRRSMKKEHRWHVEVY 402
               SCOP domains d2b5ob1 B:111-242 automated matches                                                                                                 d2b5ob2 B:243-402 automated matches                                                                                                                              SCOP domains
               CATH domains 2b5oB01 B:111-239 Translation factors                                                                                            2b5oB02 B:240-402 Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module                                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeeeeeeee.........eeeeeee............eeeee...ee...ee...eeee.............eeeeeee..eee......eeehhhhhhhhh.......eeeeeee............eeeeeee..hhhhhhhhhhhhhh..........eeeeeeee.hhhhh.hhhhhhhhhhhh...eeeeeee............hhhhhhhhhhhhhhhhhh...eeeeeeehhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh..eeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------FAD_FR  PDB: B:120-245 UniProt: 120-245                                                                                       ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2b5o B 111 SVPVNIYRPKTPFLGKCIENYELVDEGGSGTVRHVTFDISEGDLRYLEGQSIGIIPPGEDKNGKPHKLRLYSIASTRHGDMEDNKTVSLCVRQLEYQDPESGETVYGVCSTYLCNLPVGTDDVKITGPVGKEMLLPDDEDATVVMLATGTGIAPFRAFLWRMFKEQHEDYKFKGKAWLIFGVPYTANILYKDDFEKMAAENPDNFRLTYAISREQKTADGGKVYVQSRVSEYADELFEMIQKPNTHVYMCGLKGMQPPIDETFTAEAEKRGLNWEEMRRSMKKEHRWHVEVY 402
                                   120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400
   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 Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2B5O)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (FENR_SYNP2 | P31973)
molecular function
    GO:0004324    ferredoxin-NADP+ reductase activity    Catalysis of the reaction: reduced ferredoxin + NADP+ = oxidized ferredoxin + NADPH + H+.
    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.
cellular component
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0030089    phycobilisome    Any of the granules, approximately 32 nm x 48 nm and consisting of highly aggregated phycobiliproteins, that are attached in arrays to the external face of a thylakoid membrane in algae of the phyla Cyanophyta and Rhodophyta, where they function as light-harvesting devices in photosynthesis. Excitation energy in the phycobilisome flows in the sequence: phycoerythrin, phycocyanin, allophycocyanin before passing to the antenna chlorophyll of photosystem II.
    GO:0009579    thylakoid    A membranous cellular structure that bears the photosynthetic pigments in plants, algae, and cyanobacteria. In cyanobacteria thylakoids are of various shapes and are attached to, or continuous with, the plasma membrane. In eukaryotes they are flattened, membrane-bounded disk-like structures located in the chloroplasts; in the chloroplasts of higher plants the thylakoids form dense stacks called grana. Isolated thylakoid preparations can carry out photosynthetic electron transport and the associated phosphorylation.
    GO:0042651    thylakoid membrane    The pigmented membrane of any thylakoid.

 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 ]
    SO4  [ 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 ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2b5o)
 
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
  2b5o
    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
  FENR_SYNP2 | P31973
    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)
  1.18.1.2
    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
  FENR_SYNP2 | P31973
    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 2B5O)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2B5O)