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(-) Description

Title :  CRYSTAL STRUCTURE OF AVIDIN COMPLEX WITH A FERROCENE BIOTIN DERIVATIVE
 
Authors :  P. Strzelczyk, G. Bujacz
Date :  15 Jan 16  (Deposition) - 18 Jan 17  (Release) - 18 Jan 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Glycoprotein, Complex, Biotin-Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Blauz, B. Rychlik, A. Makal, K. Szulc, P. Strzelczyk, G. Bujacz, J. Zakrzewski, K. Wozniak, D. Plazuk
Ferrocene-Biotin Conjugates: Synthesis, Structure, Cytotoxi Activity And Interaction With Avidin
Chempluschem V. 81 1191 2016
PubMed: search  |  Reference-DOI: 10.1002/CPLU.201600320

(-) 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
1B9F4Ligand/Ion[(1,2,3,4,5-ETA)-CYCLOPENTADIENYL]{(1,2,3,4,5-ETA)-1-[1-HYDROXY-5-(2-OXOHEXAHYDRO-1H-THIENO[3,4-D]IMIDAZOL-4-YL)PENTYL]CYCLOPENTADIENYL}IRON
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 , THR A:38 , TRP A:70 , SER A:73 , SER A:75 , THR A:77 , TRP A:97 , SER A:101 , ARG A:114 , ASN A:118 , TRP C:110 , LYS C:111binding site for residue B9F A 201
2AC2SOFTWAREASN B:12 , SER B:16 , TYR B:33 , THR B:35 , TRP B:70 , SER B:73 , SER B:75 , THR B:77 , TRP B:97 , ARG B:114 , ASN B:118 , TRP D:110binding site for residue B9F B 201
3AC3SOFTWAREASN C:12 , LEU C:14 , SER C:16 , TYR C:33 , THR C:35 , TRP C:70 , SER C:73 , SER C:75 , THR C:77 , TRP C:97 , ARG C:114 , ASN C:118binding site for residue B9F C 301
4AC4SOFTWARETRP B:110 , ASN D:12 , LEU D:14 , 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 , THR D:77 , TRP D:97 , SER D:101 , ARG D:114 , ASN D:118binding site for residue B9F D 201
5AC5SOFTWARELYS A:9 , ASN A:17 , ILE A:34binding site for Mono-Saccharide NAG A 202 bound to ASN A 17
6AC6SOFTWAREGLY B:15 , ASN B:17 , ILE B:34 , THR B:35 , ALA B:36binding site for Mono-Saccharide NAG B 202 bound to ASN B 17
7AC7SOFTWARELYS C:9 , ASN C:17 , LEU C:123binding site for Mono-Saccharide NAG C 302 bound to ASN C 17
8AC8SOFTWARELYS D:9 , GLY D:15 , ASN D:17 , ALA D:36binding site for Mono-Saccharide NAG D 202 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 5HLM)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5HLM)

(-) 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:114
                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeee....eeee.......eeeeeee.........eeeeeee.....eeeeeee......eeeeeeeeeee...eeeeeeeeeee....hhhhhhh.eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 5hlm A   3 KCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYITAVTNEIKESPLHGTQNTTQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGINIFTRL 123
                                    12        22        32     || 45        55|       69        79        89        99       109       119    
                                                              38|           55|                                                               
                                                               42            60                                                               


Chain B from PDB  Type:PROTEIN  Length:108
                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeee....eeee.......eeeeeee......eeeeeee....eeeeeee......eeeeeeeee.....eeeeeeeee....hhhhhhh.eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 5hlm B   3 KCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYITAVIKESPLHGTQNTQPTFGFTVNWKFSESTTVFTGQCFIDGKEVLKTMWLLRSSVNDIGDDWKATRVGINIFTRL 123
                                    12        22        32    ||  48      ||63        73        83  ||    95       105       115        
                                                             37|         55|                       86|                                  
                                                              44          61                        89                                  


Chain C from PDB  Type:PROTEIN  Length:118
                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee....eeee.......eeeeeee........eeeeeee.........eeeeeee......eeeeeeeeee.....eeeeeeeeee....hhhhhhh.eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 5hlm C   2 RKCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYITAVNEIKESPLHGTQNTINKRTQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGINIFTRL 123
                                    11        21        31     || 45        55        65        75        85        95       105       115        
                                                              37|                                                                                 
                                                               42                                                                                 


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.........eeeeeee......eeeeeeeeee.....eeeeeeeeee....hhhhhhh.eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hlm D   3 KCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYITAVTATSNEIKESPLHGTQNTINKRTQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGINIFTRL 123
                                    12        22        32        42        52        62        72        82        92       102       112       122
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 5HLM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)

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  5hlm
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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 5iru 5irw

(-) Related Entries Specified in the PDB File

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