Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Theor.Model - manually
(-)Theoretical Model
collapse expand < >
Image Theor.Model - manually
Theor.Model - manually  (Jmol Viewer)
Image Theoretical Model
Theoretical Model  (Jmol Viewer)

(-) Description

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
    Engineered: YES
 
Molecule 2 - 
    Chains: B
    Engineered: YES
 
Molecule 3 - 
    Chains: 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 1BBF)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1BBF)

(-) 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
                                    66    
             STP_SHV2C   57 GPPGPPGPPGPPGL 70
               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
                  1bbf A  1 xPPGPPGPPGPPGx 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
                  1bbf 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
                                    64    
             STP_SHV2C   55 PPGPPGPPGPPGPP 68
               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
                  1bbf C  1 xPGPPGPPGPPGPx 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 1BBF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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.

 Visualization

(-) Interactive Views

Theoretical Model
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    ACE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NME  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 1bbf)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1bbf)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Theoretical Model PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1bbf
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  STP_SHV2C | P22576
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  STP_SHV2C | P22576
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

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

(-) Related Entries Specified in the PDB File

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