Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - manually
(-)NMR Structure - model 1
(-)NMR Structure - model 1, sites
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - manually
NMR Structure - manually  (Jmol Viewer)
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - model 1, sites
NMR Structure - model 1, sites  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  SOLUTION STRUCTURE OF THE ANALOGUE RETRO-INVERSO (MA-R) REGRIGGC IN CONTACT WITH THE MONOCLONAL ANTIBODY MAB 4X11, NMR, 6 STRUCTURES
 
Authors :  A. Phan Chan Du, M. C. Petit, G. Guichard, J. P. Briand, S. Muller, T. Cung
Date :  26 Aug 99  (Deposition) - 03 Sep 99  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (6x)
Keywords :  Pseudomimetic, Synthetic Peptide, Retro-Inverso Analogue, Tr-Noe, Antigen- Antibody Complex, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Phan-Chan-Du, M. C. Petit, G. Guichard, J. P. Briand, S. Muller, M. T. Cung
Structure Of Antibody-Bound Peptides And Retro-Inverso Analogues. A Transferred Nuclear Overhauser Effect Spectroscopy And Molecular Dynamics Approach.
Biochemistry V. 40 5720 2001
PubMed-ID: 11341837  |  Reference-DOI: 10.1021/BI001151H
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HISTONE H3
    ChainsA
    EngineeredYES
    FragmentC-TERMINAL DOMAIN 130-135
    Other DetailsTHE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE CGG WAS ADDED AS A LINKER TO THE DEXTRAN MATRIX IN BIACORE EXPERIMENTS VIA THE CYS THIOL GROUP. NH2-CO WAS ADDED AT THE C-TERMINAL EXTREMITY OF THE RETRO-INVERSO PEPTIDE IN ORDER TO MIMIC THE N-TERMINAL OF THE PARENT PEPTIDE. ALL NON GLYCINE RESIDUES PRESENT A D- CONFIGURATION EXCEPT CYS. TWO RI(MA) DIASTEREISOMERS WERE OBTAINED AND COULDN'T BE SEPARATED.
    SyntheticYES

 Structural Features

(-) Chains, Units

  
NMR Structure (6x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 6)

NMR Structure (5, 6)
No.NameCountTypeFull Name
1DAR2Mod. Amino AcidD-ARGININE
2DGL1Mod. Amino AcidD-GLUTAMIC ACID
3DIL1Mod. Amino AcidD-ISOLEUCINE
4DXX1Ligand/IonMETHYLMALONIC ACID
5NH21Mod. Amino AcidAMINO GROUP

(-) Sites  (1, 1)

NMR Structure (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREDAR A:2 , DGL A:3BINDING SITE FOR RESIDUE DXX A 1

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1CW8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1CW8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1CW8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1CW8)

(-) Exons   (0, 0)

(no "Exon" information available for 1CW8)

(-) Sequences/Alignments

NMR Structure
   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:9
                                        
               SCOP domains d1cw8a_   SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ......... Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                  1cw8 A  2 xxGxxGGCx 10
                            || ||   |
                            || ||   |
                            2-DAR   |
                             3-DGL  |
                               5-DAR|
                                6-DIL
                                   10-NH2

   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  (1, 1)

NMR Structure
(-)
Class: Peptides (792)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1CW8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1CW8)

(-) Gene Ontology  (0, 0)

NMR Structure(hide GO term definitions)
    (no "Gene Ontology" information available for 1CW8)

 Visualization

(-) Interactive Views

NMR Structure
  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
    DAR  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    DGL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    DIL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    DXX  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NH2  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1cw8)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1cw8
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  (no 'UniProt ID/Accession number' available) |
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  (no 'UniProt ID/Accession number' available) |
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 1CW8)

(-) Related Entries Specified in the PDB File

1cs9 1CS9 IS THE PARENT PEPTIDE.
1ct6 1CT6 IS A PARENT ANALOGUE PEPTIDE OF THE IRGERA SEQUENCE. (IN THIS PEPTIDE, ALA WAS REPLACED BY GLY).
1cvq 1 CVQ IS THE RETRO-INVERSO ANALOGUE OF 1CT6.