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(-) Description

Title :  THE STRUCTURE OF BD OXIDASE FROM GEOBACILLUS THERMODENITRIFICANS
 
Authors :  S. Safarian, H. Mueller, C. Rajendran, J. Preu, S. Ovchinnikov, T. Kusu T. Hirose, J. Langer, J. Sakamoto, H. Michel
Date :  11 Sep 15  (Deposition) - 04 May 16  (Release) - 04 May 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.05
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Bd Oxidase, Terminal Oxidase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Safarian, H. Mueller, C. Rajendran, J. Preu, S. Ovchinnikov, T. Kusumoto, J. Langer, T. Hirose, J. Sakamoto, H. Michel
The Structure Of Bd Oxidase From Geobacillus Stearothermophilus
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - BD-TYPE QUINOL OXIDASE SUBUNIT I
    Chains: A
    Organism Scientific: GEOBACILLUS THERMODENITRIFICANS (STRAIN NG80- 2)
    Organism Taxid: 420246
    Strain: NG80-2
 
Molecule 2 - BD-TYPE QUINOL OXIDASE SUBUNIT II
    Chains: B
    Organism Scientific: GEOBACILLUS THERMODENITRIFICANS (STRAIN NG80- 2)
    Organism Taxid: 420246
    Strain: NG80-2
 
Molecule 3 - PUTATIVE MEMBRANE PROTEIN
    Chains: C
    Organism Scientific: GEOBACILLUS SP. PA-3
    Organism Taxid: 1699078

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1HDD1Ligand/IonCIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE
2HEB2Ligand/IonHEME B/C

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:183 , HIS A:186 , THR A:190 , GLY A:238 , SER A:241 , GLY A:242 , LEU A:245 , LYS A:252 , MET A:325 , VAL A:326 , GLY A:329 , ALA A:366 , ALA A:369 , ILE A:370 , GLY A:373 , TRP A:374 , ALA A:377binding site for residue HEB A 501
2AC2SOFTWAREHIS A:21 , TYR A:24 , ALA A:25 , VAL A:65 , GLY A:68 , VAL A:69 , GLY A:72 , THR A:73 , ILE A:75 , GLY A:76 , GLU A:101 , THR A:102 , PHE A:105 , ILE A:146 , HDD A:503 , ASN B:60 , VAL B:61binding site for residue HEB A 502
3AC3SOFTWAREARG A:11 , GLU A:15 , LEU A:18 , THR A:19 , ILE A:22 , TRP A:83 , ILE A:146 , THR A:147 , ASN A:150 , MET A:153 , TRP A:374 , TYR A:375 , GLU A:378 , ARG A:381 , GLN A:382 , HEB A:502binding site for residue HDD A 503

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5DOQ)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Pro A:156 -Gln A:157
2Tyr B:281 -Pro B:282

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5DOQ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5DOQ)

(-) Exons   (0, 0)

(no "Exon" information available for 5DOQ)

(-) 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:432
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eee..eee..hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........eeeeeee.....eeeeeee..............................hhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5doq A   1 MNGYDPVLLSRILTELTLTVHIIYATIGVGVPLMIAIAQWVGIRKNDMHYILLARRWTRGFVITVAVGVVTGTAIGLQLSLLWPNFMQLAGQVISLPLFMETFAFFFEAIFLGIYLYTWDRFENQKKHLLLLIPVAIGSSASAMFITMVNAFMNTPQGFELKNGELVNIDPIVAMFNPAMPTKVAHVLATSYMTSAFVLASIAAWHLWKGNRHIYHRKALHLTMKTAFIFSVASALVGDLSGKFLAEYQPEKLAAAEWHFETSSHAPLILFGTLEEDNEVKYALEIPYALSILAHNHPAAVVTGLNDIPEDERPPLYIHYLFDVMVTIGVFLMVVAAVYWLGSIFRWKWTAKNWFFGLLVAGGPLAMIAIEAGWYLAEVGRQPWILRGYMKTAEGATTSAHVDTMLVLFCLLYIVLVIASATVLIRMFRRNP 432
                                    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  


Chain B from PDB  Type:PROTEIN  Length:330
                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhh....hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5doq B   1 MTLEVIGISVLWLFLFGYIIVASIDFGAGFFSVYSHWANQQHILHRIIQRYLSPVWEVTNVFLVFFFVGIVGFFPKTAYYYGSILLVPASIAIVLLAIRGSYYAFHTYGETERNWYLLAYGLTGLFIPASLSIVLTISEGGFVEENAAGVALDYGKLFASPLSWSVVLLSVTSVLYISAVFLTYYADAAGDEQARALLRRYALLWSGPTMLSALLIIYQLRYHNPEHYDNLWNVAWMLVISFLFFVITVWLLGRQRRFGWAFIALLFQYAFAFYAYGISHYPYLLYPYLTIYDGFTNETMAMALIVAFIAGLLLLIPSLYLLMRLFLFNK 330
                                    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


Chain C from PDB  Type:PROTEIN  Length:30
                                                              
               SCOP domains ------------------------------ SCOP domains
               CATH domains ------------------------------ CATH domains
               Pfam domains ------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------ PROSITE
                 Transcript ------------------------------ Transcript
                 5doq C 766 FLIMYAPMVVVALSVVAAFWVGLKDVHVNE 795
                                   775       785       795
   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)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5DOQ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5DOQ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5DOQ)

(-) Gene Ontology  (3, 5)

Asymmetric/Biological Unit(hide GO term definitions)

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        A0A0Q0UXS2_9 | A0A0Q0UXS2: 5ir6

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