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(-) Description

Title :  THE STRUCTURE OF BRADAVIDIN2-BIOTIN COMPLEX
 
Authors :  O. Livnah, A. Meir
Date :  07 Aug 12  (Deposition) - 19 Jun 13  (Release) - 10 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Bradavidin, Avidin, Oligomeric State, Streptavidin, High Affinity Systems, Lipocalin Fold, Beta Barrel, Biotin Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Leppiniemi, A. Meir, N. Kahkonen, S. Kukkurainen, J. A. Maatta, M. Ojanen, J. Janis, M. S. Kulomaa, O. Livnah, V. P. Hytonen
The Highly Dynamic Oligomeric Structure Of Bradavidin Ii Is Unique Among Avidin Proteins.
Protein Sci. V. 22 980 2013
PubMed-ID: 23661323  |  Reference-DOI: 10.1002/PRO.2281

(-) Compounds

Molecule 1 - BRADAVIDIN 2
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21-AI
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 19-130
    Gene: BLL1558
    Organism Scientific: BRADYRHIZOBIUM JAPONICUM
    Organism Taxid: 224911
    Strain: USDA 110
    Synonym: BLL1558 PROTEIN

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1BTN4Ligand/IonBIOTIN
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1BTN1Ligand/IonBIOTIN
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1BTN1Ligand/IonBIOTIN
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1BTN1Ligand/IonBIOTIN
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1BTN1Ligand/IonBIOTIN

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:15 , ARG A:17 , SER A:19 , PHE A:35 , ASN A:37 , ALA A:39 , ALA A:43 , PHE A:66 , CYS A:69 , SER A:71 , THR A:73 , TRP A:75 , TRP A:88 , ASP A:106 , HOH A:1030 , LYS D:96BINDING SITE FOR RESIDUE BTN A 900
2AC2SOFTWAREASN B:15 , SER B:19 , PHE B:35 , ASN B:37 , ALA B:39 , PHE B:42 , ALA B:43 , PHE B:66 , CYS B:69 , SER B:71 , THR B:73 , TRP B:75 , TRP B:88 , LEU B:90 , ASP B:106 , HOH B:1057 , LYS C:96BINDING SITE FOR RESIDUE BTN B 900
3AC3SOFTWARELYS B:96 , ASN C:15 , ARG C:17 , SER C:19 , PHE C:35 , ASN C:37 , ALA C:39 , ALA C:43 , PHE C:66 , CYS C:69 , SER C:71 , THR C:73 , TRP C:75 , TRP C:88 , ASP C:106 , HOH C:1029BINDING SITE FOR RESIDUE BTN C 900
4AC4SOFTWARELYS A:96 , ASN D:15 , ARG D:17 , SER D:19 , PHE D:35 , ASN D:37 , ALA D:39 , ALA D:43 , PHE D:66 , CYS D:69 , SER D:71 , THR D:73 , TRP D:75 , TRP D:88 , ASP D:106 , HOH D:1023BINDING SITE FOR RESIDUE BTN D 900

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:44 -A:69
2B:44 -B:69
3C:44 -C:69
4D:44 -D:69

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ala A:9 -Pro A:10
2Ala B:9 -Pro B:10
3Ala C:9 -Pro C:10
4Ala D:9 -Pro D:10

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4GGZ)

(-) 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:106
                                                                                                                                          
               SCOP domains d4ggza_ A: automated matches                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee....eeeeeehhh.eeeeeee...........eeeeeeeee..eeeeeeeehhh.eeeeeee.....eeeeeeeeeee.....eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 4ggz A   7 LPAPSYWKNERGSELLIWSANSGTIQGTFTNHAQGFACQGIPYPAAGSVSPTGLYFVVTFAQCNSFTRWVGTIKGSQMPTSWTLFYVDNKGKPSRLKGGDIFTRVW 112
                                    16        26        36        46        56        66        76        86        96       106      


Chain B from PDB  Type:PROTEIN  Length:106
                                                                                                                                          
               SCOP domains d4ggzb_ B: automated matches                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee....eeeeeehhh.eeeeeee...........eeeeeeeee..eeeeeeeehhh.eeeeeee.....eeeeeeeeeee.....eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 4ggz B   7 LPAPSYWKNERGSELLIWSANSGTIQGTFTNHAQGFACQGIPYPAAGSVSPTGLYFVVTFAQCNSFTRWVGTIKGSQMPTSWTLFYVDNKGKPSRLKGGDIFTRVW 112
                                    16        26        36        46        56        66        76        86        96       106      


Chain C from PDB  Type:PROTEIN  Length:106
                                                                                                                                          
               SCOP domains d4ggzc_ C: automated matches                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee....eeeeeehhh.eeeeeee...........eeeeeeeee..eeeeeeeehhhheeeeeee.....eeeeeeeeeee.....eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 4ggz C   7 LPAPSYWKNERGSELLIWSANSGTIQGTFTNHAQGFACQGIPYPAAGSVSPTGLYFVVTFAQCNSFTRWVGTIKGSQMPTSWTLFYVDNKGKPSRLKGGDIFTRVW 112
                                    16        26        36        46        56        66        76        86        96       106      


Chain D from PDB  Type:PROTEIN  Length:106
                                                                                                                                          
               SCOP domains d4ggzd_ D: automated matches                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee....eeeeeehhh.eeeeeee...........eeeeeeeee..eeeeeeeehhhheeeeeee.....eeeeeeeeeee.....eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 4ggz D   7 LPAPSYWKNERGSELLIWSANSGTIQGTFTNHAQGFACQGIPYPAAGSVSPTGLYFVVTFAQCNSFTRWVGTIKGSQMPTSWTLFYVDNKGKPSRLKGGDIFTRVW 112
                                    16        26        36        46        56        66        76        86        96       106
   Legend:   → Mismatch (orange background)
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  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, 4)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4GGZ)

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 Related Entries

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UniProtKB/TrEMBL
        Q89U61_BRADU | Q89U61: 4ggr 4ggt

(-) Related Entries Specified in the PDB File

2y32 4ggr 4ggt