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(-) Description

Title :  STRUCTURE OF GAPDH WITH CP12 PEPTIDE FROM THERMOSYNECHOCOCCUS ELONGATUS
 
Authors :  C. A. R. Cotton, J. W. Murray
Date :  26 Nov 12  (Deposition) - 11 Dec 13  (Release) - 11 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.34
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  B,C  (1x)
Biol. Unit 2:  A,D  (1x)
Keywords :  Oxidoreductase, Calvin Cycle, Photosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. A. R. Cotton, J. W. Murray
Structure Of Gapdh
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
    Chains: A, B
    EC Number: 1.2.1.13
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: KRX
    Expression System Taxid: 562
    Expression System Vector: PRSETA
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMOSYNECHOCOCCUS ELONGATUS
    Organism Taxid: 146786
    Synonym: GAPDH
 
Molecule 2 - CP12 POLYPEPTIDE
    Chains: C, D
    Fragment: C-TERMINAL, RESIDUES 53-75
    Organism Scientific: THERMOSYNECHOCOCCUS ELONGATUS
    Organism Taxid: 146786
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x):  BC 
Biological Unit 2 (1x): A  D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:8 , PHE A:9 , GLY A:10 , ARG A:11 , ILE A:12 , ASN A:35 , ASP A:36 , THR A:37 , ARG A:81 , ALA A:99 , THR A:100 , GLY A:101 , PHE A:103 , THR A:123 , ALA A:124 , CYS A:154 , ASN A:317 , TYR A:321 , HOH A:2001 , HOH A:2002 , HOH A:2003 , HOH A:2033 , HOH A:2067 , HOH A:2070 , HOH B:2037 , ASP D:66 , ARG D:71 , TYR D:73BINDING SITE FOR RESIDUE NAD A1001
2AC2SOFTWAREHOH A:2038 , HOH A:2039 , GLY B:8 , PHE B:9 , GLY B:10 , ARG B:11 , ILE B:12 , ASN B:35 , ASP B:36 , THR B:37 , ARG B:81 , ALA B:99 , THR B:100 , GLY B:101 , PHE B:103 , THR B:123 , ALA B:124 , CYS B:154 , ASN B:317 , TYR B:321 , HOH B:2002 , HOH B:2003 , HOH B:2029 , HOH B:2065 , HOH B:2068 , HOH B:2069 , HOH B:2070 , ASP C:66 , ARG C:71 , TYR C:73BINDING SITE FOR RESIDUE NAD B1001

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1C:61 -C:70
2D:61 -D:70

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3ZDF)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3ZDF)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3ZDF)

(-) Exons   (0, 0)

(no "Exon" information available for 3ZDF)

(-) Sequences/Alignments

Asymmetric 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:338
 aligned with Q8DIW5_THEEB | Q8DIW5 from UniProtKB/TrEMBL  Length:337

    Alignment length:338
                             1                                                                                                                                                                                                                                                                                                                                                
                             |       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        
         Q8DIW5_THEEB     - -MVRVAINGFGRIGRNFMRCWLQRKANSKLEIVGINDTSDPRTNAHLLKYDSMLGIFQDAEITADDDCIYAGGHAVKCVSDRNPENLPWSAWGIDLVIEATGVFTSREGASKHLSAGAKKVLITAPGKGNIPTYVVGVNHHTYDPSEDIVSNASCTTNCLAPIVKVLHEAFGIQQGMMTTTHSYTGDQRLLDASHRDLRRARAAAMNIVPTSTGAAKAVGLVIPELQGKLNGIALRVPTPNVSVVDFVAQVEKPTIAEQVNQVIKEASETTMKGIIHYSELELVSSDYRGHNASSILDASLTMVLGGNLVKVVAWYDNEWGYSQRVLDLAEHMAAHWA 337
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhhhhhhhhhhh.eeeeeee...hhhhhhhhhhh...........eee...eeee..eeeeee...hhhhhhhhhhh..eeee......hhhhhhhhhhh...eeee...............hhhhh.....eee..hhhhhhhhhhhhhhhhhhheeeeeeeeeee.........................eeee.hhhhhhhhhhhhhh..eeeeeeee.....eeeeeeeee....hhhhhhhhhhhhhhh.....eeee....hhhhhh.....eeee.hhheee...eeeeeeee..hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zdf A   0 SMVRVAINGFGRIGRNFMRCWLQRKANSKLEIVGINDTSDPRTNAHLLKYDSMLGIFQDAEITADDDCIYAGGHAVKCVSDRNPENLPWSAWGIDLVIEATGVFTSREGASKHLSAGAKKVLITAPGKGNIPTYVVGVNHHTYDPSEDIVSNASCTTNCLAPIVKVLHEAFGIQQGMMTTTHSYTGDQRLLDASHRDLRRARAAAMNIVPTSTGAAKAVGLVIPELQGKLNGIALRVPTPNVSVVDFVAQVEKPTIAEQVNQVIKEASETTMKGIIHYSELELVSSDYRGHNASSILDASLTMVLGGNLVKVVAWYDNEWGYSQRVLDLAEHMAAHWA 337
                                     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        


Chain B from PDB  Type:PROTEIN  Length:338
 aligned with Q8DIW5_THEEB | Q8DIW5 from UniProtKB/TrEMBL  Length:337

    Alignment length:338
                             1                                                                                                                                                                                                                                                                                                                                                
                             |       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        
         Q8DIW5_THEEB     - -MVRVAINGFGRIGRNFMRCWLQRKANSKLEIVGINDTSDPRTNAHLLKYDSMLGIFQDAEITADDDCIYAGGHAVKCVSDRNPENLPWSAWGIDLVIEATGVFTSREGASKHLSAGAKKVLITAPGKGNIPTYVVGVNHHTYDPSEDIVSNASCTTNCLAPIVKVLHEAFGIQQGMMTTTHSYTGDQRLLDASHRDLRRARAAAMNIVPTSTGAAKAVGLVIPELQGKLNGIALRVPTPNVSVVDFVAQVEKPTIAEQVNQVIKEASETTMKGIIHYSELELVSSDYRGHNASSILDASLTMVLGGNLVKVVAWYDNEWGYSQRVLDLAEHMAAHWA 337
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhhhhhhhhhhh.eeeeeee...hhhhhhhhhhh...........eee...eeee..eeeeee...hhhhh........eeee......hhhhhhhhhhh...eeee...............hhhhh.....eee..hhhhhhhhhhhhhhhhhhheeeeeeeeeee...................hhhhh.eeee.hhhhhhhhhhhhhh..eeeeeeee.....eeeeeeeee....hhhhhhhhhhhhhhh.....eeee....hhhhhh.....eeee.hhheee...eeeeeeee..hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zdf B   0 SMVRVAINGFGRIGRNFMRCWLQRKANSKLEIVGINDTSDPRTNAHLLKYDSMLGIFQDAEITADDDCIYAGGHAVKCVSDRNPENLPWSAWGIDLVIEATGVFTSREGASKHLSAGAKKVLITAPGKGNIPTYVVGVNHHTYDPSEDIVSNASCTTNCLAPIVKVLHEAFGIQQGMMTTTHSYTGDQRLLDASHRDLRRARAAAMNIVPTSTGAAKAVGLVIPELQGKLNGIALRVPTPNVSVVDFVAQVEKPTIAEQVNQVIKEASETTMKGIIHYSELELVSSDYRGHNASSILDASLTMVLGGNLVKVVAWYDNEWGYSQRVLDLAEHMAAHWA 337
                                     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        


Chain C from PDB  Type:PROTEIN  Length:21
 aligned with Q8DHX3_THEEB | Q8DHX3 from UniProtKB/TrEMBL  Length:75

    Alignment length:21
                                    64        74 
         Q8DHX3_THEEB    55 TSFQQYCDDNPDAAECRIYDD  75
               SCOP domains --------------------- SCOP domains
               CATH domains --------------------- CATH domains
               Pfam domains --------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) --------------------- SAPs(SNPs)
                    PROSITE --------------------- PROSITE
                 Transcript --------------------- Transcript
                 3zdf C  55 TSFQQYCDDNPDAAECRIYDD  75
                                    64        74 


Chain D from PDB  Type:PROTEIN  Length:23
 aligned with Q8DHX3_THEEB | Q8DHX3 from UniProtKB/TrEMBL  Length:75

    Alignment length:23
                                    62        72   
         Q8DHX3_THEEB    53 HKTSFQQYCDDNPDAAECRIYDD  75
               SCOP domains ----------------------- SCOP domains
               CATH domains ----------------------- CATH domains
               Pfam domains ----------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ----------------------- SAPs(SNPs)
                    PROSITE ----------------------- PROSITE
                 Transcript ----------------------- Transcript
                 3zdf D  53 HKTSFQQYCDDNPDAAECRIYDD  75
                                    62        72
   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 3ZDF)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3ZDF)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3ZDF)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q8DIW5_THEEB | Q8DIW5)
molecular function
    GO:0051287    NAD binding    Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
    GO:0050661    NADP binding    Interacting selectively and non-covalently with nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH.
    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: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:0016620    oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces NAD or NADP.
biological process
    GO:0006006    glucose metabolic process    The chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. D-glucose is dextrorotatory and is sometimes known as dextrose; it is an important source of energy for living organisms and is found free as well as combined in homo- and hetero-oligosaccharides and polysaccharides.
    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.

Chain C,D   (Q8DHX3_THEEB | Q8DHX3)

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 Related Entries

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

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        Q8DIW5_THEEB | Q8DIW5: 3zcx 4boy

(-) Related Entries Specified in the PDB File

3zcx STRUCTURE OF GAPDH FROM THERMOSYNECHOCOCCUS ELONGATUS