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Title :  ENERGY PARAMETERS IN POLYPEPTIDES. 10. IMPROVED GEOMETRICAL PARAMETERS AND NONBONDED INTERACTIONS FOR USE IN THE ECEPP(SLASH)3 ALGORITHM, WITH APPLICATION TO PROLINE-CONTAINING PEPTIDES
 
Authors :  G. Nemethy, K. D. Gibson, K. A. Palmer, C. N. Yoon, G. Paterlini, A. Zagari, S. Rumsey, H. A. Scheraga
Date :  29 Apr 92  (Deposition) - 31 Jan 94  (Release) - 15 Jan 95  (Revision)
Method :  THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  A,B,C
Keywords :  Glycoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Nemethy, K. D. Gibson, K. A. Palmer, C. N. Yoon, G. Paterlini, A. Zagari, S. Rumsey, H. A. Scheraga
Energy Parameters In Polypeptides. 10. Improved Geometrical Parameters And Nonbonded Interactions For Use In The Ecepp(Slash)3 Algorithm, With Application To Proline-Containing Peptides
J. Phys. Chem. V. 96 6472 1992
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 
    Chains: A, B, C
    Engineered: YES

 Structural Features

(-) Chains, Units

  
Theoretical Model : 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Theoretical Model (2, 6)
No.NameCountTypeFull Name
1ACE3Mod. Amino AcidACETYL GROUP
2NME3Mod. Amino AcidMETHYLAMINE

(-) Sites  (0, 0)

(no "Site" information available for 1BBE)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1BBE)

(-) 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:14
 aligned with STP_SHV2C | P22576 from UniProtKB/Swiss-Prot  Length:102

    Alignment length:14
                                    65    
             STP_SHV2C   56 PGPPGPPGPPGPPG 69
               SCOP domains -------------- SCOP domains
               CATH domains -------------- CATH domains
               Pfam domains -------------- Pfam domains
         Sec.struct. author .............. Sec.struct. author
                 SAPs(SNPs) -------------- SAPs(SNPs)
                    PROSITE -------------- PROSITE
                 Transcript -------------- Transcript
                  1bbe A  1 xGPPGPPGPPGPPx 14
                            |       10   |
                            |           14-NME
                            1-ACE         


Chain B from PDB  Type:PROTEIN  Length:14
 aligned with STP_SHV2C | P22576 from UniProtKB/Swiss-Prot  Length:102

    Alignment length:14
                                    65    
             STP_SHV2C   56 PGPPGPPGPPGPPG 69
               SCOP domains -------------- SCOP domains
               CATH domains -------------- CATH domains
               Pfam domains -------------- Pfam domains
         Sec.struct. author .............. Sec.struct. author
                 SAPs(SNPs) -------------- SAPs(SNPs)
                    PROSITE -------------- PROSITE
                 Transcript -------------- Transcript
                  1bbe B  1 xGPPGPPGPPGPPx 14
                            |       10   |
                            |           14-NME
                            1-ACE         


Chain C from PDB  Type:PROTEIN  Length:14
 aligned with STP_SHV2C | P22576 from UniProtKB/Swiss-Prot  Length:102

    Alignment length:14
                                    65    
             STP_SHV2C   56 PGPPGPPGPPGPPG 69
               SCOP domains -------------- SCOP domains
               CATH domains -------------- CATH domains
               Pfam domains -------------- Pfam domains
         Sec.struct. author .............. Sec.struct. author
                 SAPs(SNPs) -------------- SAPs(SNPs)
                    PROSITE -------------- PROSITE
                 Transcript -------------- Transcript
                  1bbe C  1 xGPPGPPGPPGPPx 14
                            |       10   |
                            |           14-NME
                            1-ACE
   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 1BBE)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Theoretical Model(hide GO term definitions)
Chain A,B,C   (STP_SHV2C | P22576)
biological process
    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.
cellular component
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        STP_SHV2C | P22576: 1bbf 1clg

(-) Related Entries Specified in the PDB File

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