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(-) Description

Title :  CRYSTAL STRUCTURE OF BACTERIAL EXPRESSED AVIDIN RELATED PROTEIN 4 (AVR4) C122S
 
Authors :  Y. Eisenberg-Domovich, V. P. Hytonen, M. Wilchek, E. A. Bayer, M. S. Kul O. Livnah
Date :  02 Dec 04  (Deposition) - 24 May 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.20
Chains :  Asym. Unit :  X,Y
Biol. Unit 1:  X,Y  (2x)
Keywords :  Avidin, Streptavidin, Avidin Related Protein, High Affinity, Thermal Stability, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Eisenberg-Domovich, V. P. Hytonen, M. Wilchek, E. A. Bayer, M. S. Kulomaa, O. Livnah
High-Resolution Crystal Structure Of An Avidin-Related Protein: Insight Into High-Affinity Biotin Binding And Protein Stability.
Acta Crystallogr. , Sect. D V. 61 528 2005
PubMed-ID: 15858262  |  Reference-DOI: 10.1107/S0907444905003914

(-) Compounds

Molecule 1 - AVIDIN-RELATED PROTEIN 4/5
    Chains: X, Y
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: AVR4
    Mutation: YES
    Organism Common: CHICKEN
    Organism Scientific: GALLUS GALLUS
    Organism Taxid: 9031

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1FMT6Ligand/IonFORMIC ACID
Biological Unit 1 (1, 12)
No.NameCountTypeFull Name
1FMT12Ligand/IonFORMIC ACID

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP X:68 , THR X:75 , TRP X:95 , HOH X:430BINDING SITE FOR RESIDUE FMT X 401
2AC2SOFTWAREASP X:39 , SER X:71 , HOH X:430 , HOH X:442 , HOH X:447BINDING SITE FOR RESIDUE FMT X 402
3AC3SOFTWAREHOH Y:129 , TRP Y:268 , THR Y:275BINDING SITE FOR RESIDUE FMT Y 403
4AC4SOFTWAREHOH Y:129 , HOH Y:136 , SER Y:271BINDING SITE FOR RESIDUE FMT Y 404
5AC5SOFTWAREHIS X:54 , LYS X:55 , ARG X:56 , HOH X:477 , HOH Y:23 , HOH Y:27 , HIS Y:267BINDING SITE FOR RESIDUE FMT X 405
6AC6SOFTWAREHOH Y:122 , HOH Y:144 , ASN Y:302 , TYR Y:306BINDING SITE FOR RESIDUE FMT Y 406

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1X:4 -X:81
2Y:204 -Y:281

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1Y53)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Y53)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AVIDIN_1PS00577 Avidin-like domain signature.AVR4_CHICK130-144
 		  2X:106-120
Y:306-320
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AVIDIN_1PS00577 Avidin-like domain signature.AVR4_CHICK130-144
 		  4X:106-120
Y:306-320

(-) Exons   (0, 0)

(no "Exon" information available for 1Y53)

(-) 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 X from PDB  Type:PROTEIN  Length:120
 aligned with AVR4_CHICK | P56734 from UniProtKB/Swiss-Prot  Length:150

    Alignment length:120
                                    36        46        56        66        76        86        96       106       116       126       136       146
           AVR4_CHICK    27 KCSLTGKWTNNLGSIMTIRAVNSRGEFTGTYLTAVADNPGNITLSPLLGIQHKRASQPTFGFTVHWNFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDISYDWKATRVGYNNFTRLC 146
               SCOP domains d1y53x_ X: automated matches                                                                                             SCOP domains
               CATH domains 1y53X00 X:3-122  [code=2.40.128.30, no name defined]                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeee....eeee.......eeeeeee.....hhhhh..eeeeeee.......eeeeeee......eeeeeeeeee.....eeeeeeeeee....hhhhhhh.eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------AVIDIN_1       -- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 1y53 X   3 KCSLTGKWTNNLGSIMTIRAVNSRGEFTGTYLTAVADNPGNITLSPLLGIQHKRASQPTFGFTVHWNFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDISYDWKATRVGYNNFTRLS 122
                                    12        22        32        42        52        62        72        82        92       102       112       122


Chain Y from PDB  Type:PROTEIN  Length:120
 aligned with AVR4_CHICK | P56734 from UniProtKB/Swiss-Prot  Length:150

    Alignment length:120
                                    36        46        56        66        76        86        96       106       116       126       136       146
           AVR4_CHICK    27 KCSLTGKWTNNLGSIMTIRAVNSRGEFTGTYLTAVADNPGNITLSPLLGIQHKRASQPTFGFTVHWNFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDISYDWKATRVGYNNFTRLC 146
               SCOP domains d1y53y_ Y: automated matches                                                                                             SCOP domains
               CATH domains 1y53Y00 Y:203-322  [code=2.40.128.30, no name defined]                                                                   CATH domains
           Pfam domains (1) -Avidin-1y53Y01 Y:204-320                                                                                             -- Pfam domains (1)
           Pfam domains (2) -Avidin-1y53Y02 Y:204-320                                                                                             -- Pfam domains (2)
         Sec.struct. author .....eeeee....eeee.......eeeeeee.....hhhhh..eeeeeee.......eeeeeee......eeeeeeeeee.....eeeeeeeeee....hhhhhhh.eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------AVIDIN_1       -- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 1y53 Y 203 KCSLTGKWTNNLGSIMTIRAVNSRGEFTGTYLTAVADNPGNITLSPLLGIQHKRASQPTFGFTVHWNFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDISYDWKATRVGYNNFTRLS 322
                                   212       222       232       242       252       262       272       282       292       302       312       322
   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 Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: Avidin] (113)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain X,Y   (AVR4_CHICK | P56734)
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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  1y53
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  AVR4_CHICK | P56734
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 Related Entries

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

UniProtKB/Swiss-Prot
        AVR4_CHICK | P56734: 1y52 1y55 2fhl 2fhn 2mf6 2of8 2of9 2ofa 2ofb 3mm0 4bcs

(-) Related Entries Specified in the PDB File

1y52
1y55 C122S MUTANT OF E. COLI EXPRESSED AVIDIN RELATED PROTEIN 4 (AVR4)-BIOTIN COMPLEX