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(-) Description

Title :  PF1 VIRUS STRUCTURE: HELICAL COAT PROTEIN AND DNA WITH PARAXIAL PHOSPHATES
 
Authors :  D. J. Liu, L. A. Day
Date :  06 Apr 94  (Deposition) - 26 Jan 95  (Release) - 27 Mar 13  (Revision)
Method :  FIBER DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (35x)
Keywords :  Complex(Viral Coat Protein-Dna), Helical Virus, Virus (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. J. Liu, L. A. Day
Pf1 Virus Structure: Helical Coat Protein And Dna With Paraxial Phosphates.
Science V. 265 671 1994
PubMed-ID: 8036516

(-) Compounds

Molecule 1 - MAJOR COAT PROTEIN OF PF1 VIRUS
    Chains: A, B
    Engineered: YES
    Organism Scientific: PSEUDOMONAS PHAGE PF1
    Organism Taxid: 10871
    Strain: G8P
 
Molecule 2 - 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE
    Chains: C, D
    Engineered: YES
    Organism Scientific: PSEUDOMONAS PHAGE PF1
    Organism Taxid: 10871
    Strain: G8P

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (35x): ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1PFI)

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:44 , SER B:41 , MET B:42 , LYS B:45BINDING SITE FOR RESIDUE DC C 1
2AC2SOFTWARELYS A:45 , LYS B:45BINDING SITE FOR RESIDUE DC D 1

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1PFI)

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1PFI)

(-) 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:46
 aligned with CAPSD_BPPF1 | P03621 from UniProtKB/Swiss-Prot  Length:82

    Alignment length:46
                                    46        56        66        76      
           CAPSD_BPPF1   37 GVIDTSAVESAITDGQGDMKAIGGYIVGALVILAVAGLIYSMLRKA 82
               SCOP domains d1pfia_ A:                                     SCOP domains
               CATH domains 1pfiA00 A:1-46                                 CATH domains
               Pfam domains Phage_Coat_B-1pfiA01 A:1-46                    Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------- PROSITE
                 Transcript ---------------------------------------------- Transcript
                  1pfi A  1 GVIDTSAVESAITDGQGDMKAIGGYIVGALVILAVAGLIYSMLRKA 46
                                    10        20        30        40      


Chain B from PDB  Type:PROTEIN  Length:46
 aligned with CAPSD_BPPF1 | P03621 from UniProtKB/Swiss-Prot  Length:82

    Alignment length:46
                                    46        56        66        76      
           CAPSD_BPPF1   37 GVIDTSAVESAITDGQGDMKAIGGYIVGALVILAVAGLIYSMLRKA 82
               SCOP domains d1pfib_ B:                                     SCOP domains
               CATH domains ---------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------- PROSITE
                 Transcript ---------------------------------------------- Transcript
                  1pfi B  1 GVIDTSAVESAITDGQGDMKAIGGYIVGALVILAVAGLIYSMLRKA 46
                                    10        20        30        40      


Chain C from PDB  Type:DNA  Length:1
                         37     
                  1pfi C  1 C  1


Chain D from PDB  Type:DNA  Length:1
                         37     
                  1pfi D  1 C  1
   Legend:   → Mismatch (orange background)
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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: Coiled coil proteins (689)

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: Inovirus-Coat (9)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (CAPSD_BPPF1 | P03621)
cellular component
    GO:0019029    helical viral capsid    The protein coat that surrounds the infective nucleic acid in some virus particles; the subunits are arranged to form a protein helix with the genetic material contained within. Tobacco mosaic virus has such a capsid structure.
    GO:0033644    host cell membrane    Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0019028    viral capsid    The protein coat that surrounds the infective nucleic acid in some virus particles. It comprises numerous regularly arranged subunits, or capsomeres.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.

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 Related Entries

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UniProtKB/Swiss-Prot
        CAPSD_BPPF1 | P03621: 1ifm 1ifn 1pjf 1ql1 1ql2 1zn5 2ifm 2ifn 2klv 2ksj 2xkm 3ifm 4ifm

(-) Related Entries Specified in the PDB File

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