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(-) Description

Title :  CRYSTAL STRUCTURE OF PORCINE HEART MITOCHONDRIAL COMPLEX II BOUND WITH FLUTOLANIL
 
Authors :  S. Harada, T. Shiba, D. Sato, A. Yamamoto, M. Nagahama, A. Yone, D. K. Ina K. Sakamoto, M. Inoue, T. Honma, K. Kita
Date :  23 Mar 15  (Deposition) - 02 Mar 16  (Release) - 02 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Oxidoreductase, Succinate Dehydrogenase, Complex Ii, Inhibitor, Oxidoreductase-Oxidoreductase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. K. Inaoka, T. Shiba, D. Sato, E. O. Balogun, T. Sasaki, M. Nagahama, M. Oda, S. Matsuoka, J. Ohmori, T. Honma, M. Inoue, K. Kita, S. Harada
Structural Insights Into The Molecular Design Of Flutolanil Derivatives Targeted For Fumarate Respiration Of Parasite Mitochondria
Int J Mol Sci V. 16 15287 2015
PubMed-ID: 26198225  |  Reference-DOI: 10.3390/IJMS160715287

(-) Compounds

Molecule 1 - SUCCINATE DEHYDROGENASE [UBIQUINONE] FLAVOPROTEIN SUBUNIT, MITOCHONDRIAL
    Chains: A
    EC Number: 1.3.5.1
    Organism Common: PIG
    Organism Scientific: SUS SCROFA
    Organism Taxid: 9823
    Synonym: FLAVOPROTEIN SUBUNIT OF COMPLEX II,FP
 
Molecule 2 - SUCCINATE DEHYDROGENASE [UBIQUINONE] IRON-SULFUR SUBUNIT, MITOCHONDRIAL
    Chains: B
    EC Number: 1.3.5.1
    Organism Common: PIG
    Organism Scientific: SUS SCROFA
    Organism Taxid: 9823
    Synonym: IRON-SULFUR SUBUNIT OF COMPLEX II,IP
 
Molecule 3 - SUCCINATE DEHYDROGENASE CYTOCHROME B560 SUBUNIT, MITOCHONDRIAL
    Chains: C
    Organism Common: PIG
    Organism Scientific: SUS SCROFA
    Organism Taxid: 9823
    Synonym: SUCCINATE-UBIQUINONE OXIDOREDUCTASE CYTOCHROME B LARGE SUBUNIT,CYBL
 
Molecule 4 - SUCCINATE DEHYDROGENASE [UBIQUINONE] CYTOCHROME B SMALL SUBUNIT, MITOCHONDRIAL
    Chains: D
    Organism Common: PIG
    Organism Scientific: SUS SCROFA
    Organism Taxid: 9823
    Synonym: CYBS,CII-4,QPS3,SUCCINATE DEHYDROGENASE COMPLEX SUBUNIT D, SUCCINATE-UBIQUINONE OXIDOREDUCTASE CYTOCHROME B SMALL SUBUNIT, SUCCINATE-UBIQUINONE REDUCTASE MEMBRANE ANCHOR SUBUNIT

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 6)

Asymmetric/Biological Unit (6, 6)
No.NameCountTypeFull Name
1F3S1Ligand/IonFE3-S4 CLUSTER
2FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3FES1Ligand/IonFE2/S2 (INORGANIC) CLUSTER
4FTN1Ligand/IonN-[3-(1-METHYLETHOXY)PHENYL]-2-(TRIFLUOROMETHYL)BENZAMIDE
5HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
6SF41Ligand/IonIRON/SULFUR CLUSTER

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:26 , ALA A:27 , GLY A:28 , GLY A:29 , ALA A:30 , THR A:49 , LYS A:50 , LEU A:51 , SER A:56 , HIS A:57 , THR A:58 , ALA A:60 , ALA A:61 , GLN A:62 , GLY A:63 , GLY A:64 , TYR A:177 , PHE A:178 , ALA A:179 , ALA A:213 , THR A:214 , GLY A:215 , THR A:225 , ASP A:233 , LEU A:264 , HIS A:365 , TYR A:366 , GLY A:397 , GLU A:398 , ARG A:409 , ALA A:412 , ASN A:413 , SER A:414 , LEU A:415 , LEU A:418binding site for residue FAD A 700
2AC2SOFTWARESER B:64 , CYS B:65 , ARG B:66 , CYS B:70 , GLY B:71 , CYS B:73 , CYS B:85binding site for residue FES B 301
3AC3SOFTWARECYS B:158 , ILE B:159 , CYS B:161 , CYS B:164 , CYS B:225 , PRO B:226binding site for residue SF4 B 302
4AC4SOFTWARECYS B:168 , TYR B:178 , CYS B:215 , HIS B:216 , MET B:219 , ASN B:220 , CYS B:221binding site for residue F3S B 303
5AC5SOFTWAREHIS C:45 , ARG C:46 , GLY C:49 , LEU C:52 , SER C:53 , VAL C:56 , HIS C:101 , THR C:102 , HIS C:108 , ARG D:47 , SER D:50 , LEU D:54 , HIS D:79 , GLY D:83binding site for residue HEM C 301
6AC6SOFTWAREPRO B:169 , SER B:170 , TRP B:173 , HIS B:216 , ILE C:30 , TRP C:35 , MET C:39 , SER C:42 , ARG C:46 , ASP D:90 , TYR D:91binding site for residue FTN C 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4YXD)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4YXD)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4YXD)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4YXD)

(-) Exons   (0, 0)

(no "Exon" information available for 4YXD)

(-) 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:613
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee..eeee..hhhhhhhhhhhhhh...eeeee..hhhhhhhhhh...ee.........hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.............eeeeeeee.......eeeeee....hhhhhhhhhhhhhhh....eeee..eeeeeeee..eeeeeeee......eeeee...eee....hhhhh..........hhhhhhhhhh...ee....eeee............hhhhhh..eee......hhhhhh.......hhhhhhhhhhhhhhhh.........eeee......hhhhhhhhhhhhhhhhhhh.......eee..eeeee...ee.....eeeeee..eeeeeeeeee....ee...........hhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhh....eehhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh..ee........hhhhhhhhhhhhhhhhhhhhhhhhhhh...............................hhhhh..eeeeeee......eeeeeee..................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yxd A  10 STQYPVVDHEFDAVVVGAGGAGLRAAFGLSEAGFNTACVTKLFPTRSHTVAAQGGINAALGNMEEDNWRWHFYDTVKGSDWLGDQDAIHYMTEQAPASVVELENYGMPFSRTEDGKIYQRAFGGQSLKFGKGGQAHRCCCVADRTGHSLLHTLYGRSLRYDTSYFVEYFALDLLMENGECRGVIALCIEDGSIHRIRARNTVVATGGYGRTYFSCTSAHTSTGDGTAMVTRAGLPCQDLEFVQFHPTGIYGAGCLITEGCRGEGGILINSQGERFMERYAPVAKDLASRDVVSRSMTLEIREGRGCGPEKDHVYLQLHHLPPEQLAVRLPGISETAMIFAGVDVTKEPIPVLPTVHYNMGGIPTNYKGQVLRHVNGQDQVVPGLYACGEAACASVHGANRLGANSLLDLVVFGRACALSIAESCRPGDKVPSIKPNAGEESVMNLDKLRFANGTIRTSELRLSMQKSMQSHAAVFRVGSVLQEGCEKILRLYGDLQHLKTFDRGMVWNTDLVETLELQNLMLCALQTIYGAEARKESRGAHAREDFKERVDEYDYSKPIQGQQKKPFQEHWRKHTLSYVDVKTGKVSLEYRPVIDKTLNEADCATVPPAIRSY 622
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619   


Chain B from PDB  Type:PROTEIN  Length:239
                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee..........eeeeeeee.hhh..hhhhhhhhhhhhh..................eeee..eeee.............eeee......eee..ee.hhhhhhhhhhh...................hhhhhhh............hhhhhhhhhhhh....hhhhhhhhhhhhh.....hhhhhhhh.............hhhhhhh....hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yxd B   9 PRIKKFAIYRWDPDKTGDKPHMQTYEIDLNNCGPMVLDALIKIKNEIDSTLTFRRSCREGICGSCAMNINGGNTLACTRRIDTNLDKVSKIYPLPHMYVIKDLVPDLSNFYAQYKSIEPYLKKKDESQEGKQQYLQSIEEREKLDGLYECILCACCSTSCPSYWWNGDKYLGPAVLMQAYRWMIDSRDDFTEERLAKLQDPFSLYRCHTIMNCTGTCPKGLNPGKAIAEIKKMMATYKE 247
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238         


Chain C from PDB  Type:PROTEIN  Length:138
                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4yxd C   6 TTAKEEMERFWNKNLGSNRPLSPHITIYRWSLPMAMSICHRGTGIALSAGVSLFGLSALLLPGNFESHLELVKSLCLGPTLIYTAKFGIVFPLMYHTWNGIRHLIWDLGKGLTIPQLTQSGVVVLILTVLSSVGLAAM 143
                                    15        25        35        45        55        65        75        85        95       105       115       125       135        


Chain D from PDB  Type:PROTEIN  Length:102
                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 4yxd D  35 SSKAASLHWTGERVVSVLLLGLLPAAYLNPCSAMDYSLAAALTLHGHWGIGQVVTDYVRGDALQKVAKAGLLALSAFTFAGLCYFNYHDVGICKAVAMLWKL 136
                                    44        54        64        74        84        94       104       114       124       134
   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  (0, 0)

(no "SCOP Domain" information available for 4YXD)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4YXD)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4YXD)

(-) Gene Ontology  (26, 57)

Asymmetric/Biological Unit(hide GO term definitions)

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  4yxd
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  SDHA_PIG | Q0QF01
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  SDHB_PIG | Q007T0
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  1.3.5.1
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 Related Entries

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

UniProtKB/Swiss-Prot
        C560_PIG | D0VWV4: 1zoy 1zp0 3abv 3ae1 3ae2 3ae3 3ae4 3ae5 3ae6 3ae7 3ae8 3ae9 3aea 3aeb 3aec 3aed 3aee 3aef 3aeg 3sfd 3sfe 4ytp
        DHSD_PIG | A5GZW8: 1zoy 1zp0 3abv 3ae1 3ae2 3ae3 3ae4 3ae5 3ae6 3ae7 3ae8 3ae9 3aea 3aeb 3aec 3aed 3aee 3aef 3aeg 3sfd 3sfe 4ytp
        SDHA_PIG | Q0QF01: 1zoy 1zp0 3abv 3ae1 3ae2 3ae3 3ae4 3ae5 3ae6 3ae7 3ae8 3ae9 3aea 3aeb 3aec 3aed 3aee 3aef 3aeg 3sfd 3sfe 4ytp
        SDHB_PIG | Q007T0: 1zoy 1zp0 3abv 3ae1 3ae2 3ae3 3ae4 3ae5 3ae6 3ae7 3ae8 3ae9 3aea 3aeb 3aec 3aed 3aee 3aef 3aeg 3sfd 3sfe 4ytp

(-) Related Entries Specified in the PDB File

4ysx 4ysy 4ysz 4yt0 4ytm 4ytn 4ytp