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(-) Description

Title :  STRUCTURE OF E378D MUTANT FLAVOCYTOCHROME C3
 
Authors :  K. L. Pankhurst, C. G. Mowat, E. L. Rothery, C. S. Miles, M. D. Walkinshaw, G. A. Reid, S. K. Chapman
Date :  05 Oct 05  (Deposition) - 23 May 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Flavocytochrome C3, Fumarate Reductase, Proton Delivery, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. L. Pankhurst, C. G. Mowat, E. L. Rothery, J. M. Hudson, A. K. Jones, C. S. Miles, M. D. Walkinshaw, F. A. Armstrong, G. A. Reid, S. K. Chapman
A Proton Delivery Pathway In The Soluble Fumarate Reductase From Shewanella Frigidimarina.
J. Biol. Chem. V. 281 20589 2006
PubMed-ID: 16699170  |  Reference-DOI: 10.1074/JBC.M603077200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FUMARATE REDUCTASE FLAVOPROTEIN SUBUNIT
    ChainsA
    EC Number1.3.99.1
    EngineeredYES
    Expression SystemSHEWANELLA FRIGIDIMARINA
    Expression System PlasmidPMMB503EH
    Expression System StrainEG301
    Expression System Taxid56812
    Expression System Vector TypePLASMID
    GeneFCC
    MutationYES
    Organism ScientificSHEWANELLA FRIGIDIMARINA
    Organism Taxid56812
    SynonymFLAVOCYTOCHROME C3, FLAVOCYTOCHROME C, FCC3

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric/Biological Unit (4, 7)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2FUM1Ligand/IonFUMARIC ACID
3HEM4Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
4NA1Ligand/IonSODIUM ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:506 , MET A:507 , GLY A:508 , GLU A:534 , THR A:536 , HOH A:1865BINDING SITE FOR RESIDUE NA A 1810
2AC2SOFTWARECYS A:14 , CYS A:17 , HIS A:18 , SER A:73 , ALA A:74 , HIS A:75 , HOH A:2017 , HOH A:2022 , HOH A:2068 , HOH A:2272 , HOH A:2799 , HOH A:2800BINDING SITE FOR RESIDUE HEM A 801
3AC3SOFTWARELEU A:4 , PHE A:7 , HIS A:8 , GLN A:12 , SER A:16 , CYS A:36 , CYS A:39 , HIS A:40 , HIS A:72 , TYR A:94 , HOH A:2277 , HOH A:2506 , HOH A:2645BINDING SITE FOR RESIDUE HEM A 802
4AC4SOFTWAREHIS A:40 , LEU A:43 , HIS A:52 , ALA A:57 , HIS A:58 , VAL A:66 , ALA A:67 , CYS A:68 , CYS A:71 , HIS A:72 , PHE A:90 , ASN A:91 , MET A:92 , HEM A:804 , HOH A:1890 , HOH A:2251 , HOH A:2827BINDING SITE FOR RESIDUE HEM A 803
5AC5SOFTWAREHIS A:54 , ASN A:56 , SER A:60 , HIS A:61 , CYS A:82 , SER A:84 , CYS A:85 , HIS A:86 , PHE A:88 , LEU A:167 , GLN A:338 , VAL A:374 , LYS A:431 , LYS A:434 , HEM A:803 , HOH A:1815 , HOH A:1830 , HOH A:1850 , HOH A:1885 , HOH A:1989 , HOH A:2004 , HOH A:2012 , HOH A:2302 , HOH A:2332BINDING SITE FOR RESIDUE HEM A 804
6AC6SOFTWAREVAL A:132 , GLY A:133 , GLY A:135 , GLY A:136 , ALA A:137 , GLU A:156 , LYS A:157 , GLU A:158 , GLY A:162 , GLY A:163 , ASN A:164 , ALA A:165 , LEU A:167 , ALA A:168 , ALA A:169 , GLY A:170 , GLY A:171 , ARG A:277 , GLY A:278 , ALA A:312 , THR A:313 , GLY A:314 , THR A:336 , GLN A:338 , ASP A:344 , MET A:375 , HIS A:504 , HIS A:505 , GLY A:533 , GLU A:534 , ARG A:544 , GLY A:547 , ASN A:548 , ALA A:549 , ILE A:550 , ILE A:553 , FUM A:1806 , HOH A:1814 , HOH A:1817 , HOH A:1818 , HOH A:1819 , HOH A:1844BINDING SITE FOR RESIDUE FAD A 1805
7AC7SOFTWAREGLY A:170 , HIS A:365 , THR A:377 , ASP A:378 , ARG A:402 , HIS A:504 , ARG A:544 , GLY A:546 , GLY A:547 , FAD A:1805BINDING SITE FOR RESIDUE FUM A 1806

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2B7R)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ala A:175 -Trp A:176

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2B7R)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MULTIHEME_CYTCPS51008 Multiheme cytochrome c family profile.FRDA_SHEFR9-91  1A:9-91
FRDA_SHEFN34-116  1A:9-91

(-) Exons   (0, 0)

(no "Exon" information available for 2B7R)

(-) 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:568
 aligned with FRDA_SHEFN | Q07WU7 from UniProtKB/Swiss-Prot  Length:596

    Alignment length:568
                                    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       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585        
           FRDA_SHEFN    26 ADNLAEFHVQNQECDSCHTPDGELSNDSLTYENTQCVSCHGTLAEVAETTKHEHYNAHASHFPGEVACTSCHSAHEKSMVYCDSCHSFDFNMPYAKKWLRDEPTIAELAKDKSERQAALASAPHDTVDVVVVGSGGAGFSAAISATDSGAKVILIEKEPVIGGNAKLAAGGMNAAWTDQQKAKKITDSPELMFEDTMKGGQNINDPALVKVLSSHSKDSVDWMTAMGADLTDVGMMGGASVNRAHRPTGGAGVGAHVVQVLYDNAVKRNIDLRMNTRGIEVLKDDKGTVKGILVKGMYKGYYWVKADAVILATGGFAKNNERVAKLDPSLKGFISTNQPGAVGDGLDVAENAGGALKDMQYIQAHPTLSVKGGVMVTEAVRGNGAILVNREGKRFVNEITTRDKASAAILAQTGKSAYLIFDDSVRKSLSKIDKYIGLGVAPTADSLVKLGKMEGIDGKALTETVARYNSLVSSGKDTDFERPNLPRALNEGNYYAIEVTPGVHHTMGGVMIDTKAEVMNAKKQVIPGLYGAGEVTGGVHGANRLGGNAISDIITFGRLAGEEAAKYS 593
               SCOP domains d2b7ra1 A:1-102 Flavocytochrome c3 (respiratory fumarate reductase), N-terminal domain                --------d2b7ra2 A:111-361,A:512-568 Flavocytochrome c3 (respiratory fumarate reductase)                                                                                                                                                                            d2b7ra3 A:362-504 Flavocytochrome c3 (respiratory fumarate reductase)                                                                          -------d2b7ra2 A:111-361,A:512-568                               SCOP domains
               CATH domains 2b7rA01 A:1-99 Flavocytochrome C3; Chain A                                                         ---2b7rA02 A:103-359,A:506-568  [code=3.50.50.60, no name defined]                                                                                                                                                                                                  -----2b7rA03 A:365-502 Flavocytochrome C3; Chain A, domain 1                                                                                   ---2b7rA02 A:103-359,A:506-568  [code=3.50.50.60, no name defined] CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhh..hhhhh...........hhhhhhhhhhhhhhhhhhhh..................hhhhh........hhhhhh....................hhhhhhhhhhhhhhhh...ee..eeee..hhhhhhhhhhhhhh...eeee........hhhhh...ee...hhhhhhh....hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.....eee.........eee.....hhhhhhhhhhhhhhhhh..eee..eeeeeeee.....eeeeeeee...eeeeee..eeee.......hhhhhhhhhhhhh...........hhhhhhhhhh...ee....eeeeeeee........hhhhhh..eee............hhhhhhhhhhhhhhhheeeeeehhhhhhhhhhhhhhhhh...ee.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhh..................eeeeeeeeeeeee..eee.....eee.....eeeeeee....ee.........hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) --------MULTIHEME_CYTC  PDB: A:9-91 UniProt: 34-116                                        --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2b7r A   1 ADNLAEFHVQNQECDSCHTPDGELSNDSLTYENTQCVSCHGTLAEVAETTKHEHYNAHASHFPGEVACTSCHSAHEKSMVYCDSCHSFDFNMPYAKKWLRDEPTIAELAKDKSERQAALASAPHDTVDVVVVGSGGAGFSAAISATDSGAKVILIEKEPVIGGNAKLAAGGMNAAWTDQQKAKKITDSPELMFEDTMKGGQNINDPALVKVLSSHSKDSVDWMTAMGADLTDVGMMGGASVNRAHRPTGGAGVGAHVVQVLYDNAVKRNIDLRMNTRGIEVLKDDKGTVKGILVKGMYKGYYWVKADAVILATGGFAKNNERVAKLDPSLKGFISTNQPGAVGDGLDVAENAGGALKDMQYIQAHPTLSVKGGVMVTDAVRGNGAILVNREGKRFVNEITTRDKASAAILAQTGKSAYLIFDDSVRKSLSKIDKYIGLGVAPTADSLVKLGKMEGIDGKALTETVARYNSLVSSGKDTDFERPNLPRALNEGNYYAIEVTPGVHHTMGGVMIDTKAEVMNAKKQVIPGLYGAGEVTGGVHGANRLGGNAISDIITFGRLAGEEAAKYS 568
                                    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       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560        

Chain A from PDB  Type:PROTEIN  Length:568
 aligned with FRDA_SHEFR | P0C278 from UniProtKB/Swiss-Prot  Length:571

    Alignment length:568
                                    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       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560        
           FRDA_SHEFR     1 ADNLAEFHVQNQECDSCHTPDGELSNDSLTYENTQCVSCHGTLEEVAETTKHEHYNAHASHFPGEVACTSCHSAHEKSMVYCDSCHSFDFNMPYAKKWQRDEPTIAELAKDKSERQAALASAPHDTVDVVVVGSGGAGFSAAISATDSGAKVILIEKEPVIGGNAKLAAGGMNAAWTDQQKAKKITDSPELMFEDTMKGGQNINDPALVKVLSSHSKDSVDWMTAMGADLTDVGMMGGASVNRAHRPTGGAGVGAHVVQVLYDNAVKRNIDLRMNTRGIEVLKDDKGTVKGILVKGMYKGYYWVKADAVILATGGFAKNNERVAKLDPSLKGFISTNQPGAVGDGLDVAENAGGALKDMQYIQAHPTLSVKGGVMVTEAVRGNGAILVNREGKRFVNEITTRDKASAAILAQTGKSAYLIFDDSVRKSLSKIDKYIGLGVAPTADSLVKLGKMEGIDGKALTETVARYNSLVSSGKDTDFERPNLPRALNEGNYYAIEVTPGVHHTMGGVMIDTKAEVMNAKKQVIPGLYGAGEVTGGVHGANRLGGNAISDIITFGRLAGEEAAKYS 568
               SCOP domains d2b7ra1 A:1-102 Flavocytochrome c3 (respiratory fumarate reductase), N-terminal domain                --------d2b7ra2 A:111-361,A:512-568 Flavocytochrome c3 (respiratory fumarate reductase)                                                                                                                                                                            d2b7ra3 A:362-504 Flavocytochrome c3 (respiratory fumarate reductase)                                                                          -------d2b7ra2 A:111-361,A:512-568                               SCOP domains
               CATH domains 2b7rA01 A:1-99 Flavocytochrome C3; Chain A                                                         ---2b7rA02 A:103-359,A:506-568  [code=3.50.50.60, no name defined]                                                                                                                                                                                                  -----2b7rA03 A:365-502 Flavocytochrome C3; Chain A, domain 1                                                                                   ---2b7rA02 A:103-359,A:506-568  [code=3.50.50.60, no name defined] CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhh..hhhhh...........hhhhhhhhhhhhhhhhhhhh..................hhhhh........hhhhhh....................hhhhhhhhhhhhhhhh...ee..eeee..hhhhhhhhhhhhhh...eeee........hhhhh...ee...hhhhhhh....hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.....eee.........eee.....hhhhhhhhhhhhhhhhh..eee..eeeeeeee.....eeeeeeee...eeeeee..eeee.......hhhhhhhhhhhhh...........hhhhhhhhhh...ee....eeeeeeee........hhhhhh..eee............hhhhhhhhhhhhhhhheeeeeehhhhhhhhhhhhhhhhh...ee.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhh..................eeeeeeeeeeeee..eee.....eee.....eeeeeee....ee.........hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------MULTIHEME_CYTC  PDB: A:9-91 UniProt: 9-91                                          --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2b7r A   1 ADNLAEFHVQNQECDSCHTPDGELSNDSLTYENTQCVSCHGTLAEVAETTKHEHYNAHASHFPGEVACTSCHSAHEKSMVYCDSCHSFDFNMPYAKKWLRDEPTIAELAKDKSERQAALASAPHDTVDVVVVGSGGAGFSAAISATDSGAKVILIEKEPVIGGNAKLAAGGMNAAWTDQQKAKKITDSPELMFEDTMKGGQNINDPALVKVLSSHSKDSVDWMTAMGADLTDVGMMGGASVNRAHRPTGGAGVGAHVVQVLYDNAVKRNIDLRMNTRGIEVLKDDKGTVKGILVKGMYKGYYWVKADAVILATGGFAKNNERVAKLDPSLKGFISTNQPGAVGDGLDVAENAGGALKDMQYIQAHPTLSVKGGVMVTDAVRGNGAILVNREGKRFVNEITTRDKASAAILAQTGKSAYLIFDDSVRKSLSKIDKYIGLGVAPTADSLVKLGKMEGIDGKALTETVARYNSLVSSGKDTDFERPNLPRALNEGNYYAIEVTPGVHHTMGGVMIDTKAEVMNAKKQVIPGLYGAGEVTGGVHGANRLGGNAISDIITFGRLAGEEAAKYS 568
                                    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       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560        

   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  (3, 3)

Asymmetric/Biological Unit

(-) CATH Domains  (3, 3)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2B7R)

(-) Gene Ontology  (9, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (FRDA_SHEFN | Q07WU7)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0000104    succinate dehydrogenase activity    Catalysis of the reaction: succinate + acceptor = fumarate + reduced acceptor.
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:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

Chain A   (FRDA_SHEFR | P0C278)
molecular function
    GO:0009055    electron carrier activity    Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0000104    succinate dehydrogenase activity    Catalysis of the reaction: succinate + acceptor = fumarate + reduced acceptor.
biological process
    GO:0019645    anaerobic electron transport chain    A process in which a series of electron carriers operate together to transfer electrons from donors such as NADH and FADH2 to any of several different terminal electron acceptors other than oxygen to generate a transmembrane electrochemical gradient.
    GO:0009061    anaerobic respiration    The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which uses compounds other than oxygen (e.g. nitrate, sulfate) as the terminal electron acceptor.
    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:0030288    outer membrane-bounded periplasmic space    The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

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 Related Entries

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

UniProtKB/Swiss-Prot
        FRDA_SHEFN | Q07WU71e39 1jrx 1jry 1jrz 1kss 1ksu 1lj1 1m64 1p2e 1p2h 1q9i 1qjd 1y0p 2b7s
        FRDA_SHEFR | P0C2781e39 1jrx 1jry 1jrz 1kss 1ksu 1lj1 1m64 1p2e 1p2h 1q9i 1qjd 1y0p 2b7s

(-) Related Entries Specified in the PDB File

1qjd WILD-TYPE ENZYME
2b7s THE SAME PROTEIN, R381K MUTANT