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(-) Description

Title :  THE RECEPTOR-BINDING PROTEIN P2 OF BACTERIOPHAGE PRD1: CRYSTAL FORM I
 
Authors :  L. Xu, S. D. Benson, S. J. Butcher, D. H. Bamford, R. M. Burnett
Date :  18 Nov 02  (Deposition) - 08 Apr 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Bacteriophage Prd1, Viral Receptor-Binding, Beta-Propeller, Proline-Rich, Antibiotic-Resistance, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Xu, S. D. Benson, S. J. Butcher, D. H. Bamford, R. M. Burnett
The Receptor Binding Protein P2 Of Prd1, A Virus Targeting Antibiotic-Resistant Bacteria, Has A Novel Fold Suggesting Multiple Functions.
Structure V. 11 309 2003
PubMed-ID: 12623018  |  Reference-DOI: 10.1016/S0969-2126(03)00023-6
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ADSORPTION PROTEIN P2
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMG59
    Expression System Strain: HMS174
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: II
    Organism Scientific: ENTEROBACTERIA PHAGE PRD1
    Organism Taxid: 10658
    Synonym: RECEPTOR-BINDING PROTEIN PRD1-P2

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
2CA1Ligand/IonCALCIUM ION
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1ACT6Ligand/IonACETATE ION
2CA-1Ligand/IonCALCIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:185 , GLY A:230 , ASP A:455 , ASP A:456 , HOH A:757BINDING SITE FOR RESIDUE ACT A 560
2AC2SOFTWAREILE A:377 , HOH A:610BINDING SITE FOR RESIDUE ACT A 561
3AC3SOFTWARELEU A:52 , HIS A:53 , HOH A:709BINDING SITE FOR RESIDUE ACT A 562
4AC4SOFTWAREASP A:425 , LYS A:426 , SER A:462 , HOH A:717 , HOH A:718 , HOH A:719BINDING SITE FOR RESIDUE CA A 601

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:254 -A:277

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Asn A:126 -Pro A:127
2Pro A:205 -Pro A:206
3Pro A:208 -Pro A:209
4Asp A:250 -Pro A:251

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1N7U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1N7U)

(-) Exons   (0, 0)

(no "Exon" information available for 1N7U)

(-) 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:554
 aligned with P2_BPPRD | P27378 from UniProtKB/Swiss-Prot  Length:591

    Alignment length:554
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551    
             P2_BPPRD     2 ANFNVPKLGVFPVAAVFDIDNVPEDSSATGSRWLPSIYQGGNYWGGGPQALHAQVSNFDSSNRLPYNPRTENNPAGNCAFAFNPFGQYISNISSAQSVHRRIYGIDLNDEPLFSPNAASITNGGNPTMSQDTGYHNIGPINTAYKAEIFRPVNPLPMSDTAPDPETLEPGQTEPLIKSDGVYSNSGIASFIFDRPVTEPNPNWPPLPPPVIPIIYPTPALGIGAAAAYGFGYQVTVYRWEEIPVEFIADPETCPAQPTTDKVIIRTTDLNPEGSPCAYEAGIILVRQTSNPMNAVAGRLVPYVEDIAVDIFLTGKFFTLNPPLRITNNYFADDEVKENTVTIGNYTTTLSSAYYAVYKTDGYGGATCFIASGGAGISALVQLQDNSVLDVLYYSLPLSLGGSKAAIDEWVANNCGLFPMSGGLDKTTLLEIPRRQLEAINPQDGPGQYDLFILDDSGAYASFSSFIGYPEAAYYVAGAATFMDVENPDEIIFILRNGAGWYACEIGDALKIADDEFDSVDYFAYRGGVMFIGSARYTEGGDPLPIKYRAIIPGL 555
               SCOP domains d1n7ua_ A: Adsorption protein p2                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ----------------------------------------------------------1n7uA02 A:60-322 receptor-binding protein prd1-p2, domain 3                                                                                                                                                                                                            ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains Prd1-P2-1n7uA01 A:2-555                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Pfam domains
         Sec.struct. author .eeee.eeee..eeeeee....................hhh.ee....eeeeeeee......eee...................eee...hhhhhhhhhhhhh..........eehhhhhhhhhh...ee....eee..eee.eeeeeeee......eeeee......eeee..ee...........ee......eeee..........eeeee..hhhh.eeeeeeeeeeeeeeeeeeeee.eeeee.............eeeee.......ee..................eeeeeeeeeeeeeeeeeeeeeeeeee...eeeeeeeee..eee..eeee.....eeee..eeeeee....eeeeeee....eeeeeeeee..eeeeeeeeeehhhhh.hhhhhhhhhhhhhh..hhhhh.ee...eeeehhhhhh...........eeee............eeeee..eeeeeee.........eeeeee.....eeeee.....eee..ee....eeeee..eeeeee............eeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1n7u A   2 ANFNVPKLGVFPVAAVFDIDNVPEDSSATGSRWLPSIYQGGNYWGGGPQALHAQVSNFDSSNRLPYNPRTENNPAGNCAFAFNPFGQYISNISSAQSVHRRIYGIDLNDEPLFSPNAASITNGGNPTMSQDTGYHNIGPINTAYKAEIFRPVNPLPMSDTAPDPETLEPGQTEPLIKSDGVYSNSGIASFIFDRPVTEPNPNWPPLPPPVIPIIYPTPALGIGAAAAYGFGYQVTVYRWEEIPVEFIADPETCPAQPTTDKVIIRTTDLNPEGSPCAYEAGIILVRQTSNPMNAVAGRLVPYVEDIAVDIFLTGKFFTLNPPLRITNNYFADDEVKENTVTIGNYTTTLSSAYYAVYKTDGYGGATCFIASGGAGISALVQLQDNSVLDVLYYSLPLSLGGSKAAIDEWVANNCGLFPMSGGLDKTTLLEIPRRQLEAINPQDGPGQYDLFILDDSGAYASFSSFIGYPEAAYYVAGAATFMDVENPDEIIFILRNGAGWYACEIGDALKIADDEFDSVDYFAYRGGVMFIGSARYTEGGDPLPIKYRAIIPGL 555
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551
   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, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: no clan defined [family: Prd1-P2] (1)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A   (P2_BPPRD | P27378)
biological process
    GO:0046718    viral entry into host cell    The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
    GO:0019062    virion attachment to host cell    The process by which a virion protein binds to molecules on the host cellular surface or host cell surface projection.
cellular component
    GO:0019012    virion    The complete fully infectious extracellular virus particle.

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 Related Entries

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

UniProtKB/Swiss-Prot
        P2_BPPRD | P27378: 1n7v

(-) Related Entries Specified in the PDB File

1n7v THE SAME PROTEIN WITH DIFFERENT SPACE GROUP