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(-) Description

Title :  CRYSTAL STRUCTURES OF CUPIN SUPERFAMILY BBDUF985 FROM BRANCHIOSTOMA BELCHERI TSINGTAUENSE IN APO AND GDP-BOUND FORMS
 
Authors :  Y. Du, Y. -X. He, G. Saren, X. Zhang, S. -C. Zhang, Y. Chen, C. -Z. Zhou
Date :  02 Mar 10  (Deposition) - 02 Jun 10  (Release) - 02 Jun 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Beta Barrel, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Z. Zou, Y. Du, Y. -X. He, G. Saren, X. Zhang, Y. Chen, S. -C. Zhang
Crystal Structures Of The Apo And Gdp-Bound Forms Of A Cupin-Like Protein Bbduf985 From Branchiostoma Belcheri Tsingtauense
Proteins 2010
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE UNCHARACTERIZED PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: BRANCHIOSTOMA BELCHERI TSINGTAUENSE
    Organism Taxid: 155462
    Synonym: CUPIN SUPERFAMILY HYPOTHETICAL PROTEIN BBDUF985

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2GDP2Ligand/IonGUANOSINE-5'-DIPHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:24 , PRO A:25 , PHE A:31 , GLU A:33 , THR A:54 , ILE A:56 , PHE A:140 , ACT A:174 , HOH A:199 , HOH A:251BINDING SITE FOR RESIDUE GDP A 173
2AC2SOFTWAREHIS B:24 , PRO B:25 , PHE B:31 , GLU B:33 , ILE B:56 , PHE B:140 , PHE B:142 , ACT B:174 , HOH B:180 , HOH B:211 , HOH B:227BINDING SITE FOR RESIDUE GDP B 173
3AC3SOFTWAREHIS B:24 , ASP B:66 , HIS B:69 , GLU B:75 , PHE B:122 , GDP B:173BINDING SITE FOR RESIDUE ACT B 174
4AC4SOFTWAREHIS A:24 , ASP A:66 , HIS A:69 , GLU A:75 , GLN A:124 , GDP A:173BINDING SITE FOR RESIDUE ACT A 174

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3LZZ)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Ser A:27 -Gly A:28
2Gly A:28 -Gly A:29
3Ala A:137 -Pro A:138
4Glu B:10 -Glu B:11
5Ala B:137 -Pro B:138

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3LZZ)

(-) 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:161
 aligned with Q6WRH7_BRABE | Q6WRH7 from UniProtKB/TrEMBL  Length:172

    Alignment length:161
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169 
         Q6WRH7_BRABE    10 EEVKRLIALYELTPHPASGGWFRETYRSDVQVEAEGFDGKRSVLTMIYYLMQAGQPDPFHRVKSDETFVHNLGGSMKIHMIHPDGSYSCSILGNPLEHPEARHQVVVPRRVWFAQEVDGYCLASVLVAPGFDFKDFSLGKREELIKEYPQHRDVIMRCTSS 170
               SCOP domains d3lzza_ A: automated matches                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh.ee......eeeeeee.................eeeeeeee....eeeee...eeeeeeeee..eeeeee.....eeeeee...........eeee....eeeeee..eeeeeeeee...hhhhhee.hhhhhhhhh..hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lzz A  10 EEVKRLIALYELTPHPASGGWFRETYRSDVQVEAEGFDGKRSVLTMIYYLMQAGQPDPFHRVKSDETFVHNLGGSMKIHMIHPDGSYSCSILGNPLEHPEARHQVVVPRRVWFAQEVDGYCLASVLVAPGFDFKDFSLGKREELIKEYPQHRDVIMRCTSS 170
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169 


Chain B from PDB  Type:PROTEIN  Length:161
 aligned with Q6WRH7_BRABE | Q6WRH7 from UniProtKB/TrEMBL  Length:172

    Alignment length:161
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169 
         Q6WRH7_BRABE    10 EEVKRLIALYELTPHPASGGWFRETYRSDVQVEAEGFDGKRSVLTMIYYLMQAGQPDPFHRVKSDETFVHNLGGSMKIHMIHPDGSYSCSILGNPLEHPEARHQVVVPRRVWFAQEVDGYCLASVLVAPGFDFKDFSLGKREELIKEYPQHRDVIMRCTSS 170
               SCOP domains d3lzzb_ B: automated matches                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --Cupin_5-3lzzB01 B:12-149                                                                                                                  --------------------- Pfam domains (1)
           Pfam domains (2) --Cupin_5-3lzzB02 B:12-149                                                                                                                  --------------------- Pfam domains (2)
         Sec.struct. author .hhhhhhhhhh.ee.....eeeeeeee...ee........ee..eeeeeeee....eeeee...eeeeeeeee..eeeeee.....eeeeee...........eeee....eeeeee..eeeeeeeee...hhhhhee.hhhhhhhhh..hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lzz B  10 EEVKRLIALYELTPHPASGGWFRETYRSDVQVEAEGFDGKRSVLTMIYYLMQAGQPDPFHRVKSDETFVHNLGGSMKIHMIHPDGSYSCSILGNPLEHPEARHQVVVPRRVWFAQEVDGYCLASVLVAPGFDFKDFSLGKREELIKEYPQHRDVIMRCTSS 170
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169
   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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: Cupin (179)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3LZZ)

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  Cis Peptide Bonds
    Ala A:137 - Pro A:138   [ RasMol ]  
    Ala B:137 - Pro B:138   [ RasMol ]  
    Glu B:10 - Glu B:11   [ RasMol ]  
    Gly A:28 - Gly A:29   [ RasMol ]  
    Ser A:27 - Gly A:28   [ RasMol ]  
 

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  3lzz
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 Related Entries

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

UniProtKB/TrEMBL
        Q6WRH7_BRABE | Q6WRH7: 3loi

(-) Related Entries Specified in the PDB File

3loi THE SAME PROTEIN COMPLEXED WITH GDP.