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(-)Theoretical Model
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Theoretical Model  (Jmol Viewer)

(-) Description

Title :  ELECTROSTATIC POTENTIAL DISTRIBUTION OF THE GENE V PROTEIN FROM FF PHAGE FACILITATES COOPERATIVE DNA BINDING: A MODEL OF THE GVP-SSDNA COMPLEX
 
Authors :  Y. Guan, H. Zhang, A. H. -J. Wang
Date :  17 Nov 94  (Deposition) - 07 Feb 95  (Release) - 08 Mar 95  (Revision)
Method :  THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  A,B,C,D
Keywords :  Complex (Dna-Binding Protein/Dna) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Guan, H. Zhang, A. H. Wang
Electrostatic Potential Distribution Of The Gene V Protein From Ff Phage Facilitates Cooperative Dna Binding: A Model Of The Gvp-Ssdna Complex.
Protein Sci. V. 4 187 1995
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'-D(P*AP*AP*AP*A)-3')
    Chains: C, D
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - GENE V PROTEIN
    Chains: A, B
    Engineered: YES
    Gene: POTENTIAL
    Organism Scientific: BACTERIOPHAGE F1

 Structural Features

(-) Chains, Units

  
Theoretical Model : 

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1GPV)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1GPV)

(-) Sequences/Alignments

Theoretical Model
   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:87
 aligned with G5P_BPF1 | P69543 from UniProtKB/Swiss-Prot  Length:87

    Alignment length:87
                                    10        20        30        40        50        60        70        80       
              G5P_BPF1    1 MIKVEIKPSQAQFTTRSGVSRQGKPYSLNEQLCYVDLGNEYPVLVKITLDEGQPAYAPGLYTVHLSSFKVGQFGSLMIDRLRLVPAK 87
               SCOP domains --------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
     Sec.struct. author (1) .eeeeehhhhheeeeeeeee---eeeeeeeeeeeee.....eeeeeeeetttt......eeeeehhheeee---eeee.eeeeeee. Sec.struct. author (1)
     Sec.struct. author (2) -------------------tttt-----------------------------------------------tttt------------- Sec.struct. author (2)
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                  1gpv A  1 MIKVEIKPSQAQFTTRSGVSRQGKPYSLNEQLCYVDLGNEYPVLVKITLDEGQPAYAPGLYTVHLSSFKVGQFGSLMIDRLRLVPAK 87
                                    10        20        30        40        50        60        70        80       


Chain A from PDB  Type:PROTEIN  Length:87
 aligned with G5P_BPFD | P69542 from UniProtKB/Swiss-Prot  Length:87

    Alignment length:87
                                    10        20        30        40        50        60        70        80       
              G5P_BPFD    1 MIKVEIKPSQAQFTTRSGVSRQGKPYSLNEQLCYVDLGNEYPVLVKITLDEGQPAYAPGLYTVHLSSFKVGQFGSLMIDRLRLVPAK 87
               SCOP domains --------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
     Sec.struct. author (1) .eeeeehhhhheeeeeeeee---eeeeeeeeeeeee.....eeeeeeeetttt......eeeeehhheeee---eeee.eeeeeee. Sec.struct. author (1)
     Sec.struct. author (2) -------------------tttt-----------------------------------------------tttt------------- Sec.struct. author (2)
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                  1gpv A  1 MIKVEIKPSQAQFTTRSGVSRQGKPYSLNEQLCYVDLGNEYPVLVKITLDEGQPAYAPGLYTVHLSSFKVGQFGSLMIDRLRLVPAK 87
                                    10        20        30        40        50        60        70        80       


Chain A from PDB  Type:PROTEIN  Length:87
 aligned with G5P_BPM13 | P69544 from UniProtKB/Swiss-Prot  Length:87

    Alignment length:87
                                    10        20        30        40        50        60        70        80       
             G5P_BPM13    1 MIKVEIKPSQAQFTTRSGVSRQGKPYSLNEQLCYVDLGNEYPVLVKITLDEGQPAYAPGLYTVHLSSFKVGQFGSLMIDRLRLVPAK 87
               SCOP domains --------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
     Sec.struct. author (1) .eeeeehhhhheeeeeeeee---eeeeeeeeeeeee.....eeeeeeeetttt......eeeeehhheeee---eeee.eeeeeee. Sec.struct. author (1)
     Sec.struct. author (2) -------------------tttt-----------------------------------------------tttt------------- Sec.struct. author (2)
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                  1gpv A  1 MIKVEIKPSQAQFTTRSGVSRQGKPYSLNEQLCYVDLGNEYPVLVKITLDEGQPAYAPGLYTVHLSSFKVGQFGSLMIDRLRLVPAK 87
                                    10        20        30        40        50        60        70        80       


Chain B from PDB  Type:PROTEIN  Length:87
 aligned with G5P_BPF1 | P69543 from UniProtKB/Swiss-Prot  Length:87

    Alignment length:87
                                    10        20        30        40        50        60        70        80       
              G5P_BPF1    1 MIKVEIKPSQAQFTTRSGVSRQGKPYSLNEQLCYVDLGNEYPVLVKITLDEGQPAYAPGLYTVHLSSFKVGQFGSLMIDRLRLVPAK 87
               SCOP domains --------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeehhhhheeeeeeeee...eeeeeeeeeeeee.....eeeeeeee..........eeeeehhheeee...eeee.eeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                  1gpv B  1 MIKVEIKPSQAQFTTRSGVSRQGKPYSLNEQLCYVDLGNEYPVLVKITLDEGQPAYAPGLYTVHLSSFKVGQFGSLMIDRLRLVPAK 87
                                    10        20        30        40        50        60        70        80       


Chain B from PDB  Type:PROTEIN  Length:87
 aligned with G5P_BPFD | P69542 from UniProtKB/Swiss-Prot  Length:87

    Alignment length:87
                                    10        20        30        40        50        60        70        80       
              G5P_BPFD    1 MIKVEIKPSQAQFTTRSGVSRQGKPYSLNEQLCYVDLGNEYPVLVKITLDEGQPAYAPGLYTVHLSSFKVGQFGSLMIDRLRLVPAK 87
               SCOP domains --------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeehhhhheeeeeeeee...eeeeeeeeeeeee.....eeeeeeee..........eeeeehhheeee...eeee.eeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                  1gpv B  1 MIKVEIKPSQAQFTTRSGVSRQGKPYSLNEQLCYVDLGNEYPVLVKITLDEGQPAYAPGLYTVHLSSFKVGQFGSLMIDRLRLVPAK 87
                                    10        20        30        40        50        60        70        80       


Chain B from PDB  Type:PROTEIN  Length:87
 aligned with G5P_BPM13 | P69544 from UniProtKB/Swiss-Prot  Length:87

    Alignment length:87
                                    10        20        30        40        50        60        70        80       
             G5P_BPM13    1 MIKVEIKPSQAQFTTRSGVSRQGKPYSLNEQLCYVDLGNEYPVLVKITLDEGQPAYAPGLYTVHLSSFKVGQFGSLMIDRLRLVPAK 87
               SCOP domains --------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeehhhhheeeeeeeee...eeeeeeeeeeeee.....eeeeeeee..........eeeeehhheeee...eeee.eeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                  1gpv B  1 MIKVEIKPSQAQFTTRSGVSRQGKPYSLNEQLCYVDLGNEYPVLVKITLDEGQPAYAPGLYTVHLSSFKVGQFGSLMIDRLRLVPAK 87
                                    10        20        30        40        50        60        70        80       


Chain C from PDB  Type:DNA  Length:4
                                   
                  1gpv C  1 AAAA  4


Chain D from PDB  Type:DNA  Length:4
                                   
                  1gpv D  1 AAAA  4
   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  (0, 0)

(no "SCOP Domain" information available for 1GPV)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1GPV)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1GPV)

(-) Gene Ontology  (4, 12)

Theoretical Model(hide GO term definitions)
Chain A,B   (G5P_BPFD | P69542)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003697    single-stranded DNA binding    Interacting selectively and non-covalently with single-stranded DNA.
biological process
    GO:0006260    DNA replication    The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
    GO:0039684    rolling circle single-stranded viral DNA replication    A rolling circle viral DNA replication that begins with a single-stranded viral DNA genome.

Chain A,B   (G5P_BPM13 | P69544)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003697    single-stranded DNA binding    Interacting selectively and non-covalently with single-stranded DNA.
biological process
    GO:0006260    DNA replication    The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
    GO:0039684    rolling circle single-stranded viral DNA replication    A rolling circle viral DNA replication that begins with a single-stranded viral DNA genome.

Chain A,B   (G5P_BPF1 | P69543)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003697    single-stranded DNA binding    Interacting selectively and non-covalently with single-stranded DNA.
biological process
    GO:0006260    DNA replication    The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
    GO:0039684    rolling circle single-stranded viral DNA replication    A rolling circle viral DNA replication that begins with a single-stranded viral DNA genome.

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 Related Entries

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

UniProtKB/Swiss-Prot
        G5P_BPF1 | P69543: 1ae2 1ae3 1gkh 1gvp 1vqa 1vqb 1vqc 1vqd 1vqe 1vqf 1vqg 1vqh 1vqi 1vqj 1yha 1yhb
        G5P_BPFD | P69542: 2gn5
        G5P_BPM13 | P69544: 2gva 2gvb

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1GPV)