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(-) Description

Title :  CRYSTAL STRUCTURE OF AVIDIN - 6-(6-BIOTINAMIDOHEXANAMIDO) HEXANOYLFERROCENE COMPLEX
 
Authors :  P. Strzelczyk, A. Bujacz, G. Bujacz
Date :  05 Mar 13  (Deposition) - 20 Nov 13  (Release) - 20 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.99
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Beta Barrel, Biotin-Binding Protein, 6-(6-Biotinamidohexanamido) Hexanoylferrocene, Glycoprotein, Hen Egg White (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Plazuk, J. Zakrzewski, M. Salmain, A. Blauz, B. Rychlik, P. Strzelczyk, A. Bujacz, G. Bujacz
Ferrocene-Biotin Conjugates Targeting Cancer Cells: Synthesis, Interaction With Avidin, Cytotoxic Properties An The Crystal Structure Of The Complex Of Avidin With A Biotin-Linker-Ferrocene Conjugate
Organometallics V. 32 5774 2013
PubMed: search  |  Reference-DOI: 10.1021/OM4003126

(-) Compounds

Molecule 1 - AVIDIN
    Chains: A, B
    Organism Common: BANTAM,CHICKENS
    Organism Scientific: GALLUS GALLUS
    Organism Taxid: 9031
    Secretion: EGG WHITE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1B6F2Ligand/Ion[(1,2,3,4,5-ETA)-CYCLOPENTADIENYL][(1,2,3,4,5-ETA)-{6-[(6-{[5-(2-OXOHEXAHYDRO-1H-THIENO[3,4-D]IMIDAZOL-4-YL)PENTANOYL]AMINO}HEXANOYL)AMINO]HEXANOYL}CYCLOPENTADIENYL]IRON
2NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1B6F4Ligand/Ion[(1,2,3,4,5-ETA)-CYCLOPENTADIENYL][(1,2,3,4,5-ETA)-{6-[(6-{[5-(2-OXOHEXAHYDRO-1H-THIENO[3,4-D]IMIDAZOL-4-YL)PENTANOYL]AMINO}HEXANOYL)AMINO]HEXANOYL}CYCLOPENTADIENYL]IRON
2NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:12 , SER A:16 , TYR A:33 , THR A:35 , VAL A:37 , THR A:38 , ALA A:39 , THR A:40 , TRP A:70 , PHE A:72 , SER A:75 , THR A:77 , TRP A:97 , SER A:101 , TRP A:110 , LYS A:111 , ARG A:114 , ASN A:118 , HOH A:321 , B6F B:201BINDING SITE FOR RESIDUE B6F A 201
2AC2SOFTWAREGLY A:15 , ASN A:17 , THR A:34 , ALA B:22BINDING SITE FOR RESIDUE NAG A 202
3AC3SOFTWAREGLU A:74 , SER A:102 , ASN A:104 , B6F A:201 , HOH A:338 , ASN B:12 , LEU B:14 , SER B:16 , TYR B:33 , THR B:35 , ALA B:36 , ARG B:59 , TRP B:70 , PHE B:72 , SER B:73 , SER B:75 , THR B:77 , TRP B:97 , TRP B:110 , LYS B:111 , ASN B:118 , HOH B:335BINDING SITE FOR RESIDUE B6F B 201
4AC4SOFTWAREGLY B:15 , ASN B:17 , THR B:34 , ALA B:36 , ILE B:44 , LEU B:123BINDING SITE FOR RESIDUE NAG B 202

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:4 -A:83
2B:4 -B:83

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4JHQ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4JHQ)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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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:124
                                                                                                                                                            
               SCOP domains d4jhqa_ A: automated matches                                                                                                 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
                 4jhq A   2 RKCSLTGKWTNDLGSNMTIGAVNSKGEFTGTYTTAVTATSNEIKESPLHGTQNTINKRTQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGINIFTRLRT 125
                                    11        21        31        41        51        61        71        81        91       101       111       121    


Chain B from PDB  Type:PROTEIN  Length:123
                                                                                                                                                           
               SCOP domains d4jhqb_ B: automated matches                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee....eeee.......eeeeeeeee.......eeeeeeeeee.hhhhh...eeeeeee......eeeeeeeeee.....eeeeeeeeee....hhhhhhh.eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jhq B   2 RKCSLTGKWTNDLGSNMTIGAVNSKGEFTGTYTTAVTATSNEIKESPLHGTQNTINKRTQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGINIFTRLR 124
                                    11        21        31        41        51        61        71        81        91       101       111       121
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  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 Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)

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  4jhq
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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 4u46 5chk 5hlm 5iru 5irw

(-) Related Entries Specified in the PDB File

1vyo AVIDIN APO-FORM
2avi AVIDIN - BIOTIN COMPLEX
4i60 AVIDIN - BIOTINYLRUTHENOCENE COMPLEX