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(-) Description

Title :  AVIAN RESPIRATORY COMPLEX II WITH MALONATE BOUND
 
Authors :  L. S. Huang, J. T. Shen, A. C. Wang, E. A. Berry
Date :  06 Jun 06  (Deposition) - 20 Jun 06  (Release) - 29 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Complex Ii, Membrane Protein, Heme Protein, Iron Sulfur Protein, Cytochrome B, Oxidoreductase, Redox Enzyme, Respiratory Chain, Malonate, Ubiquinone (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. S. Huang, J. T. Shen, A. C. Wang, E. A. Berry
Crystallographic Studies Of The Binding Of Ligands To The Dicarboxylate Site Of Complex Ii, And The Identity Of The Ligand In The
Biochim. Biophys. Acta V. 1757 1073
PubMed-ID: 16935256  |  Reference-DOI: 10.1016/J.BBABIO.2006.06.015
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SUCCINATE DEHYDROGENASE FLAVOPROTEIN SUBUNIT
    Chains: A
    EC Number: 1.3.5.1
    Organism Common: CHICKEN
    Organism Scientific: GALLUS GALLUS
    Organism Taxid: 9031
 
Molecule 2 - SUCCINATE DEHYDROGENASE IP SUBUNIT
    Chains: B
    EC Number: 1.3.5.1
    Organism Common: CHICKEN
    Organism Scientific: GALLUS GALLUS
    Organism Taxid: 9031
 
Molecule 3 - SUCCINATE DEHYDROGENASE CYTOCHROME B, LARGE SUBUNIT
    Chains: C
    EC Number: 1.3.5.1
    Organism Common: CHICKEN
    Organism Scientific: GALLUS GALLUS
    Organism Taxid: 9031
 
Molecule 4 - SUCCINATE DEHYDROGENASE CYTOCHROME B, SMALL SUBUNIT
    Chains: D
    EC Number: 1.3.5.1
    Organism Common: CHICKEN
    Organism Scientific: GALLUS GALLUS
    Organism Taxid: 9031

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (10, 51)

Asymmetric/Biological Unit (10, 51)
No.NameCountTypeFull Name
1BHG1Ligand/Ion2-HEXYLOXY-6-HYDROXYMETHYL-TETRAHYDRO-PYRAN-3,4,5-TRIOL
2F3S1Ligand/IonFE3-S4 CLUSTER
3FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
4FES1Ligand/IonFE2/S2 (INORGANIC) CLUSTER
5HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
6K2Ligand/IonPOTASSIUM ION
7MLI1Ligand/IonMALONATE ION
8PEE2Ligand/Ion1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE
9SF41Ligand/IonIRON/SULFUR CLUSTER
10UNL40Ligand/IonUNKNOWN LIGAND

(-) Sites  (40, 40)

Asymmetric Unit (40, 40)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:365 , ASN A:366 , MET A:367 , GLY A:368 , GLU A:397 , ALA A:399BINDING SITE FOR RESIDUE K A 622
02AC2SOFTWAREGLY A:25 , ALA A:26 , GLY A:27 , GLY A:28 , ALA A:29 , THR A:48 , LYS A:49 , LEU A:50 , SER A:55 , HIS A:56 , THR A:57 , ALA A:59 , ALA A:60 , GLN A:61 , GLY A:62 , GLY A:63 , TYR A:176 , PHE A:177 , ALA A:178 , ALA A:212 , THR A:213 , GLY A:214 , THR A:224 , ASP A:232 , LEU A:263 , HIS A:364 , TYR A:365 , GLY A:396 , GLU A:397 , ARG A:408 , ALA A:411 , ASN A:412 , SER A:413 , LEU A:414 , LEU A:417 , MLI A:1002 , HOH A:1020 , HOH A:1029 , HOH A:1035 , HOH A:1099BINDING SITE FOR RESIDUE FAD A 1001
03AC3SOFTWAREGLY A:62 , HIS A:253 , THR A:265 , GLU A:266 , ARG A:297 , HIS A:364 , ARG A:408 , ALA A:411 , FAD A:1001BINDING SITE FOR RESIDUE MLI A 1002
04AC4SOFTWAREHIS A:326BINDING SITE FOR RESIDUE UNL A 1003
05AC5SOFTWAREGLU A:540BINDING SITE FOR RESIDUE UNL A 1004
06AC6SOFTWAREASP A:603 , ARG A:604BINDING SITE FOR RESIDUE UNL A 1006
07AC7SOFTWAREALA A:429BINDING SITE FOR RESIDUE UNL A 1007
08AC8SOFTWAREPRO A:330 , GLN A:331BINDING SITE FOR RESIDUE UNL A 1008
09AC9SOFTWAREUNL A:1010BINDING SITE FOR RESIDUE UNL A 1009
10BC1SOFTWARETRP A:78 , UNL A:1009BINDING SITE FOR RESIDUE UNL A 1010
11BC2SOFTWARESER A:620 , TYR A:621 , HOH A:1277BINDING SITE FOR RESIDUE UNL A 1011
12BC3SOFTWAREARG A:309 , GLU A:310 , GLY A:311BINDING SITE FOR RESIDUE UNL A 1013
13BC4SOFTWAREPRO A:329BINDING SITE FOR RESIDUE UNL A 1015
14BC5SOFTWAREPHE A:137 , SER A:612 , VAL A:614BINDING SITE FOR RESIDUE UNL A 1016
15BC6SOFTWAREGLY A:241BINDING SITE FOR RESIDUE UNL A 1017
16BC7SOFTWAREMET B:191 , ASP B:193 , ASP B:196 , THR B:199 , HOH B:1047 , HOH B:1081 , HOH B:1167BINDING SITE FOR RESIDUE K B 253
17BC8SOFTWARESER B:64 , CYS B:65 , ARG B:66 , GLY B:68 , CYS B:70 , GLY B:71 , SER B:72 , CYS B:73 , CYS B:85BINDING SITE FOR RESIDUE FES B 1002
18BC9SOFTWARECYS B:158 , CYS B:161 , ALA B:162 , CYS B:164 , MET B:185 , CYS B:225BINDING SITE FOR RESIDUE SF4 B 1003
19CC1SOFTWARECYS B:168 , SER B:170 , TYR B:178 , CYS B:215 , HIS B:216 , THR B:217 , ILE B:218 , MET B:219 , ASN B:220 , CYS B:221BINDING SITE FOR RESIDUE F3S B 1004
20CC2SOFTWAREILE B:11 , LYS B:13 , LEU B:93BINDING SITE FOR RESIDUE UNL B 1005
21CC3SOFTWARETRP B:173 , UNL B:1007 , UNL C:145 , TYR D:58BINDING SITE FOR RESIDUE UNL B 1006
22CC4SOFTWAREILE B:218 , UNL B:1006 , UNL C:144 , UNL C:145BINDING SITE FOR RESIDUE UNL B 1007
23CC5SOFTWAREHIS B:104BINDING SITE FOR RESIDUE UNL B 1010
24CC6SOFTWARELYS B:177BINDING SITE FOR RESIDUE UNL B 1011
25CC7SOFTWAREGLU A:121BINDING SITE FOR RESIDUE UNL B 1012
26CC8SOFTWAREASP B:208 , PRO B:209 , ALA D:6 , HOH D:1390BINDING SITE FOR RESIDUE UNL B 1013
27CC9SOFTWARELYS B:139BINDING SITE FOR RESIDUE UNL B 1014
28DC1SOFTWAREARG B:223 , LYS C:31 , TRP C:32 , SER C:33 , LEU C:34 , PRO C:35 , GLU C:120 , TYR D:88 , TYR D:89BINDING SITE FOR RESIDUE BHG C 141
29DC2SOFTWAREHIS B:216 , HIS C:42 , ARG C:43 , GLY C:46 , VAL C:47 , LEU C:49 , SER C:50 , HIS C:98 , UNL C:146 , HIS D:46 , GLY D:50 , LEU D:51BINDING SITE FOR RESIDUE HEM C 142
30DC3SOFTWARESER C:96 , LEU D:21BINDING SITE FOR RESIDUE PEE C 143
31DC4SOFTWAREUNL B:1007 , MET C:36BINDING SITE FOR RESIDUE UNL C 144
32DC5SOFTWAREUNL B:1006 , UNL B:1007 , UNL C:146 , HOH C:1145BINDING SITE FOR RESIDUE UNL C 145
33DC6SOFTWAREHEM C:142 , UNL C:145 , HOH C:1003 , HOH C:1145BINDING SITE FOR RESIDUE UNL C 146
34DC7SOFTWAREPHE C:56BINDING SITE FOR RESIDUE UNL C 148
35DC8SOFTWAREGLU C:8 , HOH C:1375BINDING SITE FOR RESIDUE UNL C 149
36DC9SOFTWAREALA C:59BINDING SITE FOR RESIDUE UNL C 152
37EC1SOFTWAREALA D:27 , TYR D:28 , VAL D:97 , TRP D:101BINDING SITE FOR RESIDUE PEE D 105
38EC2SOFTWAREHIS D:9 , HOH D:1276 , HOH D:1519BINDING SITE FOR RESIDUE UNL D 125
39EC3SOFTWAREALA D:41 , HOH D:1379BINDING SITE FOR RESIDUE UNL D 132
40EC4SOFTWARETYR D:30 , PRO D:31BINDING SITE FOR RESIDUE UNL D 142

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1B:73 -B:85

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ala A:401 -Ser A:402

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2H89)

(-) PROSITE Motifs  (5, 5)

Asymmetric/Biological Unit (5, 5)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
12FE2S_FER_2PS51085 2Fe-2S ferredoxin-type iron-sulfur binding domain profile.SDHB_CHICK50-143  1B:12-105
2FRD_SDH_FAD_BINDINGPS00504 Fumarate reductase / succinate dehydrogenase FAD-binding site.SDHA_CHICK98-107  1A:54-63
32FE2S_FER_1PS00197 2Fe-2S ferredoxin-type iron-sulfur binding region signature.SDHB_CHICK103-111  1B:65-73
44FE4S_FER_2PS51379 4Fe-4S ferredoxin-type iron-sulfur binding domain profile.SDHB_CHICK186-216  1B:148-178
54FE4S_FER_1PS00198 4Fe-4S ferredoxin-type iron-sulfur binding region signature.SDHB_CHICK196-207  1B:158-169

(-) Exons   (0, 0)

(no "Exon" information available for 2H89)

(-) 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
 aligned with SDHA_CHICK | Q9YHT1 from UniProtKB/Swiss-Prot  Length:665

    Alignment length:613
                                    62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662   
           SDHA_CHICK    53 STQYPVVDHEFDAVVVGAGGAGLRAAFGLSEAGFNTACVTKLFPTRSHTVAAQGGINAALGNMEDDNWRWHFYDTVKGSDWLGDQDAIHYMTEQAPAAVIELENYGMPFSRTEEGKIYQRAFGGQSLQFGKGGQAHRCCCVADRTGHSLLHTLYGRSLRYDTSYFVEYFALDLLMENGECRGVIALCIEDGTIHRFRAKNTVIATGGYGRTYFSCTSAHTSTGDGTAMVTRAGLPCQDLEFVQFHPTGIYGAGCLITEGCRGEGGILINSQGERFMERYAPVAKDLASRDVVSRSMTIEIREGRGCGPEKDHVYLQLHHLPPQQLATRLPGISETAMIFAGVDVTKEPIPVLPTVHYNMGGIPTNYKGQVITHVNGEDKVVPGLYACGEAASASVHGANRLGANSLLDLVVFGRACALTIAETCKPGEPVPSIKPNAGEESVANLDKLRFADGTIRTSEARLNMQKTMQSHAAVFRTGSILQEGCEKLSQIYCDLAHLKTFDRGIVWNTDLVETLELQNLMLCALQTIYGAEARKESRGAHAREDYKFRIDDFDYSKPLQGQQKRPFEEHWRKHTLSYVDVKSGKVTLKYRPVIDRTLNEEDCSSVPPAIRSY 665
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2h89A01 A:9-256,A:361-439  [code=3.50.50.60, no name defined]                                                                                                                                                                                           --------------------------------------------------------------------------------------------------------2h89A01 A:9-256,A:361-439  [code=3.50.50.60, no name defined]                  2h89A03 A:440-556  [code=1.20.58.100, no name defined]                                                               2h89A04 A:557-621 succinate dehydrogenase protein domain          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeeee..hhhhhhhhhhhhhh...eeee...hhhhhhhhhh...ee.........hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh............ee.................ee....hhhhhhhhhhhhhhh....eee..eeeeeeeee..eeeeeeeee....eeeeeeeeeeee....hhhhh..........hhhhhhhhh....ee....eeeeeeee........hhhhhh..eee......hhhhhh..hhhhhhhhhhhhhhhhhhhh..........eeee....hhhhhhhhhhhhhhhhhhhhh.......eeeeeeeeee...ee.....eeeeee..eeeeeeeeee....ee...........hhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhh....eehhhhhhhhhhhhhhhh..eehhhhhhhhhhhhhhhhhhh..ee........hhhhhhhhhhhhhhhhhhhhhhhhhhh.......ee......................hhhhh..eeeeeeee....eeeeeeee..................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---------------------------------------------FRD_SDH_FA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2h89 A   9 STQYPVVDHEFDAVVVGAGGAGLRAAFGLSEAGFNTACVTKLFPTRSHTVAAQGGINAALGNMEDDNWRWHFYDTVKGSDWLGDQDAIHYMTEQAPAAVIELENYGMPFSRTEEGKIYQRAFGGQSLQFGKGGQAHRCCCVADRTGHSLLHTLYGRSLRYDTSYFVEYFALDLLMENGECRGVIALCIEDGTIHRFRAKNTVIATGGYGRTYFSCTSAHTSTGDGTAMVTRAGLPCQDLEFVQFHPTGIYGAGCLITEGCRGEGGILINSQGERFMERYAPVAKDLASRDVVSRSMTIEIREGRGCGPEKDHVYLQLHHLPPQQLATRLPGISETAMIFAGVDVTKEPIPVLPTVHYNMGGIPTNYKGQVITHVNGEDKVVPGLYACGEAASASVHGANRLGANSLLDLVVFGRACALTIAETCKPGEPVPSIKPNAGEESVANLDKLRFADGTIRTSEARLNMQKTMQSHAAVFRTGSILQEGCEKLSQIYRDLAHLKTFDRGIVWNTDLVETLELQNLMLCALQTIYGAEARKESRGAHAREDYKLRIDEFDYSKPLQGQQKRPFEEHWRKHTLSYVDVKSGKVTLKYRPVIDRTLNEEDCSSVPPAIRSY 621
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618   


Chain B from PDB  Type:PROTEIN  Length:241
 aligned with SDHB_CHICK | Q9YHT2 from UniProtKB/Swiss-Prot  Length:290

    Alignment length:241
                                    54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284 
           SDHB_CHICK    45 ATSRIKKFSIYRWDPDKPGDKPRMQTYEVDLNKCGPMVLDALIKIKNELDSTLTFRRSCREGICGSCAMNIAGGNTLACTKKIDPDLSKTTKIYPLPHMYVVKDLVPDLSNFYAQYKSIEPYLKKKDESKQGKEQYLQSIEDRQKLDGLYECILCACCSTSCPSYWWNGDKYLGPAVLMQAYRWMIDSRDDYTEERLAQLQDPFSLYRCHTIMNCTRTCPKGLNPGKAIAEIKKMMATYKE 285
               SCOP domains d2h89b1 B:7-114 Succinate dehydogenase iron-sulfur protein, N-terminal domain                               d2h89b2 B:115-247 Succinate dehydogenase                                                                                              SCOP domains
               CATH domains 2h89B01 B:7-114  [code=3.10.20.30, no name defined]                                                         2h89B02 B:115-247 Fumarate Reductase Iron-sulfur Protein; Chain B, domain 2                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeee..........eeeeeeee.hhh..hhhhhhhhhhhhh..................eeee..eeee.............eeee......eee..ee.hhhhhhhhhh....................hhhhhhh............hhhhhhhhhhhh....hhhhhhhhhhhhh.....hhhhhhhh.............hhhhhhh....hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----2FE2S_FER_2  PDB: B:12-105 UniProt: 50-143                                                    ------------------------------------------4FE4S_FER_2  PDB: B:148-178    --------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------4FE4S_FER_1 ------------------------------------------------------------------------------ PROSITE (2)
                PROSITE (3) ----------------------------------------------------------2FE2S_FER------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (3)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2h89 B   7 ATSRIKKFSIYRWDPDKPGDKPRMQTYEVDLNKCGPMVLDALIKIKNELDSTLTFRRSCREGICGSCAMNIAGGNTLACTKKIDPDLSKTTKIYPLPHMYVVKDLVPDLSNFYAQYKSIEPYLKKKDESKQGKEQYLQSIEDRQKLDGLYECILCACCSTSCPSYWWNGDKYLGPAVLMQAYRWMIDSRDDYTEERLAQLQDPFSLYRCHTIMNCTRTCPKGLNPGKAIAEIKKMMATYKE 247
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246 


Chain C from PDB  Type:PROTEIN  Length:139
 aligned with D0VWW3_CHICK | D0VWW3 from UniProtKB/TrEMBL  Length:140

    Alignment length:139
                                    11        21        31        41        51        61        71        81        91       101       111       121       131         
         D0VWW3_CHICK     2 ATTAKEEMARFWEKNTKSSRPLSPHISIYKWSLPMAMSITHRGTGVALSLGVSLFSLAALLLPEQFPHYVAVVKSLSLSPALIYSAKFALVFPLSYHTWNGIRHLVWDMGKGFKLSQVEQSGVVVLILTLLSSAAIASE 140
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2h89C01 C:2-32 Single helix bin2h89C02 C:33-140 Fumarate reductase respiratory complex transmembrane subunits                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2h89 C   2 ATTAKEEMARFWEKNTKSSRPLSPHISIYKWSLPMAMSITHRGTGVALSLGVSLFSLAALLLPEQFPHYVAVVKSLSLSPALIYSAKFALVFPLSYHTWNGIRHLVWDMGKGFKLSQVEQSGVVVLILTLLSSAAIASE 140
                                    11        21        31        41        51        61        71        81        91       101       111       121       131         


Chain D from PDB  Type:PROTEIN  Length:102
 aligned with DHSD_CHICK | Q5ZIS0 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:102
                                    65        75        85        95       105       115       125       135       145       155  
           DHSD_CHICK    56 SSKAASLHWTSERAVSALLLGLLPAAYLYPGPAVDYSLAAALTLHGHWGLGQVITDYVHGDTPIKVANTGLYVLSAITFTGLCYFNYYDVGICKAVAMLWSI 157
               SCOP domains d2h89d_ D: automated matches                                                                           SCOP domains
               CATH domains 2h89D00 D:2-103 Fumarate reductase respiratory complex transmembrane subunits                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 2h89 D   2 SSKAASLHWTSERAVSALLLGLLPAAYLYPGPAVDYSLAAALTLHGHWGLGQVITDYVHGDTPIKVANTGLYVLSAITFTGLCYFNYYDVGICKAVAMLWSI 103
                                    11        21        31        41        51        61        71        81        91       101
   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
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Membrane and cell surface proteins and peptides (2046)

(-) CATH Domains  (7, 8)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Few Secondary Structures (1120)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2H89)

(-) Gene Ontology  (25, 51)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SDHA_CHICK | Q9YHT1)
molecular function
    GO:0050660    flavin adenine dinucleotide binding    Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
    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:0016627    oxidoreductase activity, acting on the CH-CH group of donors    Catalysis of an oxidation-reduction (redox) reaction in which a CH-CH group acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
    GO:0008177    succinate dehydrogenase (ubiquinone) activity    Catalysis of the reaction: succinate + ubiquinone = fumarate + ubiquinol.
    GO:0000104    succinate dehydrogenase activity    Catalysis of the reaction: succinate + acceptor = fumarate + reduced acceptor.
biological process
    GO:0022900    electron transport chain    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: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.
    GO:0022904    respiratory 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 to generate a transmembrane electrochemical gradient.
    GO:0006105    succinate metabolic process    The chemical reactions and pathways involving succinate, also known as butanedioate or ethane dicarboxylate, the dianion of succinic acid. Succinate is an important intermediate in metabolism and a component of the TCA cycle.
    GO:0006099    tricarboxylic acid cycle    A nearly universal metabolic pathway in which the acetyl group of acetyl coenzyme A is effectively oxidized to two CO2 and four pairs of electrons are transferred to coenzymes. The acetyl group combines with oxaloacetate to form citrate, which undergoes successive transformations to isocitrate, 2-oxoglutarate, succinyl-CoA, succinate, fumarate, malate, and oxaloacetate again, thus completing the cycle. In eukaryotes the tricarboxylic acid is confined to the mitochondria. See also glyoxylate cycle.
cellular component
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005743    mitochondrial inner membrane    The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae.
    GO:0005749    mitochondrial respiratory chain complex II, succinate dehydrogenase complex (ubiquinone)    A protein complex located in the mitochondrial inner membrane that forms part of the mitochondrial respiratory chain. Contains the four polypeptide subunits of succinate dehydrogenase, flavin-adenine dinucleotide and iron-sulfur. Catalyzes the oxidation of succinate by ubiquinone. Connects the TCA cycle with the respiratory chain.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

Chain B   (SDHB_CHICK | Q9YHT2)
molecular function
    GO:0051537    2 iron, 2 sulfur cluster binding    Interacting selectively and non-covalently with a 2 iron, 2 sulfur (2Fe-2S) cluster; this cluster consists of two iron atoms, with two inorganic sulfur atoms found between the irons and acting as bridging ligands.
    GO:0051538    3 iron, 4 sulfur cluster binding    Interacting selectively and non-covalently with a 3 iron, 4 sulfur (3Fe-4S) cluster; this cluster consists of three iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands. It is essentially a 4Fe-4S cluster with one iron missing.
    GO:0051539    4 iron, 4 sulfur cluster binding    Interacting selectively and non-covalently with a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
    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:0051536    iron-sulfur cluster binding    Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
    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:0008177    succinate dehydrogenase (ubiquinone) activity    Catalysis of the reaction: succinate + ubiquinone = fumarate + ubiquinol.
    GO:0048039    ubiquinone binding    Interacting selectively and non-covalently with ubiquinone, a quinone derivative with a tail of isoprene units.
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.
    GO:0006099    tricarboxylic acid cycle    A nearly universal metabolic pathway in which the acetyl group of acetyl coenzyme A is effectively oxidized to two CO2 and four pairs of electrons are transferred to coenzymes. The acetyl group combines with oxaloacetate to form citrate, which undergoes successive transformations to isocitrate, 2-oxoglutarate, succinyl-CoA, succinate, fumarate, malate, and oxaloacetate again, thus completing the cycle. In eukaryotes the tricarboxylic acid is confined to the mitochondria. See also glyoxylate cycle.
cellular component
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005743    mitochondrial inner membrane    The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae.
    GO:0005749    mitochondrial respiratory chain complex II, succinate dehydrogenase complex (ubiquinone)    A protein complex located in the mitochondrial inner membrane that forms part of the mitochondrial respiratory chain. Contains the four polypeptide subunits of succinate dehydrogenase, flavin-adenine dinucleotide and iron-sulfur. Catalyzes the oxidation of succinate by ubiquinone. Connects the TCA cycle with the respiratory chain.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

Chain C   (D0VWW3_CHICK | D0VWW3)
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:0016627    oxidoreductase activity, acting on the CH-CH group of donors    Catalysis of an oxidation-reduction (redox) reaction in which a CH-CH group acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
    GO:0008177    succinate dehydrogenase (ubiquinone) activity    Catalysis of the reaction: succinate + ubiquinone = fumarate + ubiquinol.
    GO:0000104    succinate dehydrogenase activity    Catalysis of the reaction: succinate + acceptor = fumarate + reduced acceptor.
biological process
    GO:0006099    tricarboxylic acid cycle    A nearly universal metabolic pathway in which the acetyl group of acetyl coenzyme A is effectively oxidized to two CO2 and four pairs of electrons are transferred to coenzymes. The acetyl group combines with oxaloacetate to form citrate, which undergoes successive transformations to isocitrate, 2-oxoglutarate, succinyl-CoA, succinate, fumarate, malate, and oxaloacetate again, thus completing the cycle. In eukaryotes the tricarboxylic acid is confined to the mitochondria. See also glyoxylate cycle.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0045281    succinate dehydrogenase complex    A multimeric complex which consists of flavoprotein (subunit A ; InterPro:IPR003952), iron-sulfur protein (subunit B) and membrane-bound cytochrome b560 (subunit C; InterPro:IPR000701). In some Archaea, the membrane-bound subunits (C or C and D) do not necessarily contain heme. Membrane-bound subunits can bind or react with quinones.

Chain D   (DHSD_CHICK | Q5ZIS0)
molecular function
    GO:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000104    succinate dehydrogenase activity    Catalysis of the reaction: succinate + acceptor = fumarate + reduced acceptor.
    GO:0048039    ubiquinone binding    Interacting selectively and non-covalently with ubiquinone, a quinone derivative with a tail of isoprene units.
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.
    GO:0006099    tricarboxylic acid cycle    A nearly universal metabolic pathway in which the acetyl group of acetyl coenzyme A is effectively oxidized to two CO2 and four pairs of electrons are transferred to coenzymes. The acetyl group combines with oxaloacetate to form citrate, which undergoes successive transformations to isocitrate, 2-oxoglutarate, succinyl-CoA, succinate, fumarate, malate, and oxaloacetate again, thus completing the cycle. In eukaryotes the tricarboxylic acid is confined to the mitochondria. See also glyoxylate cycle.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005740    mitochondrial envelope    The double lipid bilayer enclosing the mitochondrion and separating its contents from the cell cytoplasm; includes the intermembrane space.
    GO:0005743    mitochondrial inner membrane    The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae.
    GO:0005749    mitochondrial respiratory chain complex II, succinate dehydrogenase complex (ubiquinone)    A protein complex located in the mitochondrial inner membrane that forms part of the mitochondrial respiratory chain. Contains the four polypeptide subunits of succinate dehydrogenase, flavin-adenine dinucleotide and iron-sulfur. Catalyzes the oxidation of succinate by ubiquinone. Connects the TCA cycle with the respiratory chain.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DHSD_CHICK | Q5ZIS0: 1yq3 1yq4 2fbw 2h88 2wqy
        SDHA_CHICK | Q9YHT1: 1yq3 1yq4 2fbw 2h88 2wqy
        SDHB_CHICK | Q9YHT2: 1yq3 1yq4 2fbw 2h88 2wqy
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        D0VWW3_CHICK | D0VWW3: 1yq3 1yq4 2fbw 2h88 2wqy

(-) Related Entries Specified in the PDB File

1yq3 AVIAN COMPLEX II FROM ORTHORHOMBIC CRYSTAL FORM
1yq4 AVIAN COMPLEX II, 3-NITROPROPIONIC ACID-MODIFIED
1zoy PORCINE COMPLEX II FROM ORTHORHOMBIC CRYSTAL
1zp0 PORCINE COMPLEX II WITH 3-NITROPROPIONATE AND TTFA BOUND
2fbw AVIAN COMPLEX II WITH CARBOXIN BOUND