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(-) Description

Title :  CRYSTAL STRUCTURE OF DEPHOSPHORYLATED PIG HEART, GTP-SPECIFIC SUCCINYL-COA SYNTHETASE
 
Authors :  M. E. Fraser, M. N. G. James, W. A. Bridger, W. T. Wolodko
Date :  14 Apr 00  (Deposition) - 27 Jul 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ligase, Gtp-Specific (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. E. Fraser, M. N. James, W. A. Bridger, W. T. Wolodko
Phosphorylated And Dephosphorylated Structures Of Pig Heart, Gtp-Specific Succinyl-Coa Synthetase.
J. Mol. Biol. V. 299 1325 2000
PubMed-ID: 10873456  |  Reference-DOI: 10.1006/JMBI.2000.3807
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SUCCINYL-COA SYNTHETASE, ALPHA CHAIN
    ChainsA
    EC Number6.2.1.4
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-3B
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism CommonPIG
    Organism ScientificSUS SCROFA
    Organism Taxid9823
    SynonymSCS-ALPHA
    TissueHEART
 
Molecule 2 - SUCCINYL-COA SYNTHETASE, BETA CHAIN
    ChainsB
    EC Number6.2.1.4
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-3B
    Expression System Taxid562
    Expression System Vector TypePLASMID
    MutationYES
    Organism CommonPIG
    Organism ScientificSUS SCROFA
    Organism Taxid9823
    SynonymSCS-BETA
    TissueHEART

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 5)

Asymmetric/Biological Unit (4, 5)
No.NameCountTypeFull Name
1CME1Mod. Amino AcidS,S-(2-HYDROXYETHYL)THIOCYSTEINE
2PO41Ligand/IonPHOSPHATE ION
3SO42Ligand/IonSULFATE ION
4ZN1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:162 , GLY A:163 , THR A:164 , HIS A:259 , HOH A:318 , HOH A:325 , HOH A:326 , GLY B:272 , ALA B:273 , GLY B:274BINDING SITE FOR RESIDUE PO4 A 307
2AC2SOFTWAREARG A:255 , ARG A:256 , MET B:0 , ASP B:227BINDING SITE FOR RESIDUE SO4 A 308
3AC3SOFTWAREGLY B:53 , ARG B:54BINDING SITE FOR RESIDUE SO4 B 396
4AC4SOFTWARECYS B:268 , ALA B:276 , CYS B:280 , ASN B:292 , HOH B:448BINDING SITE FOR RESIDUE ZN B 400

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1EUC)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Gly A:129 -Pro A:130
2Gly A:236 -Pro A:237
3Asn B:206 -Pro B:207

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1EUC)

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SUCCINYL_COA_LIG_1PS01216 ATP-citrate lyase / succinyl-CoA ligases family signature 1.SUCA_PIG200-229  1A:160-189
2SUCCINYL_COA_LIG_2PS00399 ATP-citrate lyase / succinyl-CoA ligases family active site.SUCA_PIG288-301  1A:248-261
3SUCCINYL_COA_LIG_3PS01217 ATP-citrate lyase / succinyl-CoA ligases family signature 3.SUCB2_PIG302-327  1B:264-289

(-) Exons   (0, 0)

(no "Exon" information available for 1EUC)

(-) 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:306
 aligned with SUCA_PIG | O19069 from UniProtKB/Swiss-Prot  Length:346

    Alignment length:306
                                    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      
             SUCA_PIG    41 CSYTASRKHLYVDKNTKVICQGFTGKQGTFHSQQALEYGTNLVGGTTPGKGGKTHLGLPVFNTVKEAKEQTGATASVIYVPPPFAAAAINEAIDAEVPLVVCITEGIPQQDMVRVKHRLLRQGKTRLIGPNCPGVINPGECKIGIMPGHIHKKGRIGIVSRSGTLTYEAVHQTTQVGLGQSLCVGIGGDPFNGTDFTDCLEIFLNDPATEGIILIGEIGGNAEENAAEFLKQHNSGPKSKPVVSFIAGLTAPPGRRMGHAGAIIAGGKGGAKEKITALQSAGVVVSMSPAQLGTTIYKEFEKRKML 346
               SCOP domains d1euca1 A:1-130 Succinyl-CoA synthetase, alpha-chain, N-terminal (CoA-binding) domain                                             d1euca2 A:131-306 Succinyl-CoA synthetase, alpha-chain, C-terminal domain                                                                                                        SCOP domains
               CATH domains --------1eucA01 A:9-131 NAD(P)-binding Rossmann-like Domain                                                                        1eucA02 A:132-301  [code=3.40.50.261, no name defined]                                                                                                                    ----- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhh.....eeeee...hhhhhhhhhhhhhhh.eeeeee.......ee..eeee.hhhhhhhhhh..eeee..hhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhh.....eee.....eeee...eeee..hhhhh....eeeee.hhhhhhhhhhhhhhh...eeeeee.........hhhhhhhhhhhh....eeeeeee...hhhhhhhhhhhhhh.......eeeeee......................hhhhhhhhhhhh..ee..hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------SUCCINYL_COA_LIG_1            ----------------------------------------------------------SUCCINYL_COA_L--------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1euc A   1 CSYTASRKHLYVDKNTKVICQGFTGKQGTFHSQQALEYGTNLVGGTTPGKGGKTHLGLPVFNTVKEAKEQTGATASVIYVPPPFAAAAINEAIDAEVPLVVCITEGIPQQDMVRVKHRLLRQGKTRLIGPNCPGVINPGECKIGIMPGHIHKKGRIGIVSRSGTLTYEAVHQTTQVGLGQSLCVGIGGDPFNGTDFTDCLEIFLNDPATEGIILIGEIGGNAEENAAEFLKQHNSGPKSKPVVSFIAGLTAPPGRRMGHAGAIIAGGKGGAKEKITALQSAGVVVSMSPAQLGTTIYKEFEKRKML 306
                                    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      

Chain B from PDB  Type:PROTEIN  Length:394
 aligned with SUCB2_PIG | P53590 from UniProtKB/Swiss-Prot  Length:433

    Alignment length:394
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427    
            SUCB2_PIG    38 WLNLQEYQSKKLMSDNGVKVQRFFVADTANEALEAAKRLNAKEIVLKAQILAGGRGKGVFSSGLKGGVHLTKDPEVVGQLAKQMIGYNLATKQTPKEGVKVNKVMVAEALDISRETYLAILMDRSCNGPVLVGSPQGGVDIEEVAASNPELIFKEQIDIIEGIKDSQAQRMAENLGFLGPLQNQAADQIKKLYNLFLKIDATQVEVNPFGETPEGQVVCFDAKINFDDNAEFRQKDIFAMDDKSENEPIENEAAKYDLKYIGLDGNIACFVNGAGLAMATCDIIFLNGGKPANFLDLGGGVKESQVYQAFKLLTADPKVEAILVNIFGGIVNCAIIANGITKACRELELKVPLVVRLEGTNVHEAQNILTNSGLPITSAVDLEDAAKKAVASVT 431
               SCOP domains d1eucb2 B:0-245 Succinyl-CoA synthetase, beta-chain, N-terminal domain                                                                                                                                                                                d1eucb1 B:246-393 Succinyl-CoA synthetase, beta-chain, C-terminal domain                                                                             SCOP domains
               CATH domains -1eucB01             1eucB02 B:21-111 ATP-grasp fold, A domain                                                  1eucB01 B:1-20,B:112-246 ATP-grasp fold, B domain                                                                                      1eucB03 B:247-392  [code=3.40.50.261, no name defined]                                                                                            - CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhh.......eeee.hhhhhhhhhhhhh...eeeee..........ee.......eeee.hhhhhhhhhhh....eee........ee...eeeee.....eeeeeeeeeehhhheeeeeee.....hhhhhhhhhhhhheeee.......hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeee...eeee..eeeee.hhhhhhhhhhhhh......hhhhhhhhhh..eeee....eeeee.hhhhhhhhhhhhhhh.....eeee.....hhhhhhhhhhhh.......eeeeeee......hhhhhhhhhhhhhhh....eeeeee..hhhhhhhhhhh....eee..hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SUCCINYL_COA_LIG_3        -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1euc B   0 MVNLQEYQSKKLMSDNGVKVQRFFVADTANEALEAAKRLNAKEIVLKAQILAGGRGKGVFSSGLKGGVHLTKDPEVVGQLAKQMIGYNLATKQTPKEGVKVNKVMVAEALDISRETYLAILMDRSCNGPVLVGSPQGGVDIEEVAASNPELIFKEQIDIIEGIKDSQAQRMAENLGFLGPLQNQAADQIKKLYNLFLKIDATQVEVNPFGETPEGQVVCFDAKINFDDNAEFRQKDIFAMDDKSENEPIENEAAKYDLKYIGLDGNIACFVNGAGLAMATCDIIFLNGGKPANFLDLGGGVKESQVYQAFKLLTADPKVEAILVNIFGGIVNcAIIANGITKACRELELKVPLVVRLEGTNVHEAQNILTNSGLPITSAVDLEDAAKKAVASVT 393
                                     9        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    
                                                                                                                                                                                                                                                                                                                                                                      332-CME                                                         

   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  (4, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (4, 5)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1EUC)

(-) Gene Ontology  (16, 24)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SUCA_PIG | O19069)
molecular function
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0048037    cofactor binding    Interacting selectively and non-covalently with a cofactor, a substance that is required for the activity of an enzyme or other protein. Cofactors may be inorganic, such as the metal atoms zinc, iron, and copper in certain forms, or organic, in which case they are referred to as coenzymes. Cofactors may either be bound tightly to active sites or bind loosely with the substrate.
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0004775    succinate-CoA ligase (ADP-forming) activity    Catalysis of the reaction: ATP + succinate + CoA = ADP + succinyl-CoA + phosphate.
    GO:0004776    succinate-CoA ligase (GDP-forming) activity    Catalysis of the reaction: GTP + succinate + CoA = GDP + succinyl-CoA + phosphate.
biological process
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0009142    nucleoside triphosphate biosynthetic process    The chemical reactions and pathways resulting in the formation of a nucleoside triphosphate, a compound consisting of a nucleobase linked to a deoxyribose or ribose sugar esterified with triphosphate on the sugar.
    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:0006104    succinyl-CoA metabolic process    The chemical reactions and pathways involving succinyl-CoA, a compound composed of the monovalent acyl group 3-carboxypropanoyl, derived from succinic acid by loss of one OH group, linked to coenzyme A.
    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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005759    mitochondrial matrix    The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
    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   (SUCB2_PIG | P53590)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0004776    succinate-CoA ligase (GDP-forming) activity    Catalysis of the reaction: GTP + succinate + CoA = GDP + succinyl-CoA + phosphate.
biological process
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    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: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
        SUCA_PIG | O190691eud 2fp4 2fpg 2fpi 2fpp 4xx0 5cae
        SUCB2_PIG | P535901eud 2fp4 2fpg 2fpi 2fpp 4xx0 5cae

(-) Related Entries Specified in the PDB File

1cqi 1CQI IS CRYSTAL STRUCTURE OF THE COMPLEX OF ADP AND MG2+ WITH DEPHOSPHORYLATED E. COLI SUCCINYL-COA SYNTHETASE
1cqj 1CQJ IS CRYSTAL STRUCTURE OF DEPHOSPHORYLATED E. COLI SUCCINYL-COA SYNTHETASE
1eud 1EUD IS CRYSTAL STRUCTURE OF PHOSPHORYLATED PIG HEART, GTP- SPECIFIC SUCCINYL-COA SYNTHETASE
2scu 2SCU IS PHOSPHORYLATED SUCCINYL-COA SYNTHETASE FROM E. COLI