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(-) Description

Title :  CRYSTAL STRUCTURE OF AVIDIN IN COMPLEX WITH 1-DESTHIOBIOTINYLPYRENE
 
Authors :  P. Strzelczyk, G. Bujacz
Date :  14 Mar 16  (Deposition) - 12 Oct 16  (Release) - 19 Oct 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Complex, Biotin Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Strzelczyk, D. Plazuk, J. Zakrzewski, G. Bujacz
Structural Characterization Of The Avidin Interactions With Fluorescent Pyrene-Conjugates: 1-Biotinylpyrene And 1-Desthiobiotinylpyrene.
Molecules V. 21 2016
PubMed-ID: 27689976  |  Reference-DOI: 10.3390/MOLECULES21101270

(-) Compounds

Molecule 1 - AVIDIN
    Chains: A, B, C, D
    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  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1D9P4Ligand/Ion1-DESTHIOBIOTINYLPYRENE
2NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:12 , SER A:16 , TYR A:33 , THR A:35 , VAL A:37 , ALA A:39 , THR A:40 , TRP A:70 , SER A:73 , SER A:75 , TRP A:97 , ASN A:118binding site for residue D9P A 202
2AC2SOFTWAREASN B:12 , SER B:16 , TYR B:33 , THR B:35 , VAL B:37 , THR B:38 , ALA B:39 , THR B:40 , TRP B:70 , SER B:75 , TRP B:97 , SER B:101 , ASN B:118 , TRP D:110binding site for residue D9P B 202
3AC3SOFTWARETRP A:110 , ASN C:12 , SER C:16 , TYR C:33 , THR C:35 , THR C:38 , ALA C:39 , THR C:40 , TRP C:70 , SER C:73 , TRP C:97 , SER C:101 , ASN C:118 , GLU D:43 , LYS D:45binding site for residue D9P C 202
4AC4SOFTWARETRP B:110 , HOH B:320 , ASN D:12 , SER D:16 , TYR D:33 , THR D:35 , THR D:38 , ALA D:39 , THR D:40 , TRP D:70 , SER D:73 , SER D:75 , TRP D:97 , SER D:101 , ARG D:114 , ASN D:118binding site for residue D9P D 202
5AC5SOFTWAREASN A:17 , LEU A:123 , HOH A:301binding site for Mono-Saccharide NAG A 201 bound to ASN A 17
6AC6SOFTWARELYS B:9 , ASN B:17 , THR B:34 , LEU B:123 , HOH B:302 , HOH B:314binding site for Mono-Saccharide NAG B 201 bound to ASN B 17
7AC7SOFTWAREARG A:26 , GLY C:15 , ASN C:17 , LEU C:123binding site for Mono-Saccharide NAG C 201 bound to ASN C 17
8AC8SOFTWARELYS D:9 , GLY D:15 , ASN D:17 , THR D:34 , LEU D:123binding site for Mono-Saccharide NAG D 201 bound to ASN D 17

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:4 -A:83
2B:4 -B:83
3C:4 -C:83
4D:4 -D:83

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5IRW)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5IRW)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5IRW)

(-) Exons   (0, 0)

(no "Exon" information available for 5IRW)

(-) 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:121
                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee....eeee.......eeeeeee............eeeeeee.hhhhh...eeeeeee......eeeeeeeeee.....eeeeeeeeee....hhhhhhh.eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 5irw A   3 KCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYTTAVTATSNEIKESPLHGTQNTINKRTQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGINIFTRL 123
                                    12        22        32        42        52        62        72        82        92       102       112       122 


Chain B from PDB  Type:PROTEIN  Length:121
                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee....eeee.......eeeeeee............eeeeeee.hhhhh...eeeeeee......eeeeeeeeee.....eeeeeeeeee....hhhhhhh.eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 5irw B   3 KCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYTTAVTATSNEIKESPLHGTQNTINKRTQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGINIFTRL 123
                                    12        22        32        42        52        62        72        82        92       102       112       122 


Chain C from PDB  Type:PROTEIN  Length:121
                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee....eeee.......eeeeeee............eeeeeee.hhhhh...eeeeeee......eeeeeeeeee.....eeeeeeeeee....hhhhhhh.eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 5irw C   3 KCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYTTAVTATSNEIKESPLHGTQNTINKRTQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGINIFTRL 123
                                    12        22        32        42        52        62        72        82        92       102       112       122 


Chain D from PDB  Type:PROTEIN  Length:121
                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee....eeee.......eeeeeee............eeeeeee.hhhhh...eeeeeee......eeeeeeeeee.....eeeeeeeeee....hhhhhhh.eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 5irw D   3 KCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYTTAVTATSNEIKESPLHGTQNTINKRTQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGINIFTRL 123
                                    12        22        32        42        52        62        72        82        92       102       112       122
   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  (0, 0)

(no "SCOP Domain" information available for 5IRW)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5IRW)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5IRW)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)

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  5irw
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  AVID_CHICK | P02701
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 Related Entries

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

UniProtKB/Swiss-Prot
        AVID_CHICK | P02701: 1avd 1ave 1ij8 1ldo 1ldq 1lel 1nqn 1rav 1vyo 2a5b 2a5c 2a8g 2avi 2c4i 2cam 2jgs 2mf6 3fdc 3mm0 3vgw 3vhh 3vhi 3vhm 4i60 4jhq 4u46 5chk 5hlm 5iru

(-) Related Entries Specified in the PDB File

1vyo AVIDIN, FREE-LIGAND STRUCTURE
3vgw MONOAC-BIOTIN - AVIDIN COMPLEX
4i60 AVIDIN - BIOTINYLRUTHENOCENE COMPLEX