Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
(-)Biological Unit 3
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)

(-) Description

Title :  THE STRUCTURE OF THE M53A MUTANT OF THE CAULOBACTER CRESCENTUS CLPS IN COMPLEX WITH A PEPTIDE CONTAINING AN AMINO-TERMINAL NORLEUCINE RESIDUE
 
Authors :  T. A. Baker, G. Roman-Hernandez, R. T. Sauer, R. A. Grant
Date :  02 Feb 09  (Deposition) - 09 Mar 10  (Release) - 09 Mar 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.48
Chains :  Asym. Unit :  A,B,D
Biol. Unit 1:  A,B,D  (1x)
Biol. Unit 2:  A  (1x)
Biol. Unit 3:  B,D  (1x)
Keywords :  Adaptor, Protein-Peptide Complex, Peptide-Binding Protein, Peptide Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Roman-Hernandez, R. A. Grant, R. T. Sauer, T. A. Baker
Structure Of Caulobacter Crescentus Clps In Complex With Various Peptides
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ATP-DEPENDENT CLP PROTEASE ADAPTER PROTEIN CLPS
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET23B
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CC_2467, CLPS
    Mutation: YES
    Organism Common: CAULOBACTER VIBRIOIDES
    Organism Scientific: CAULOBACTER VIBRIOIDES
    Organism Taxid: 155892
    Strain: CB15
 
Molecule 2 - PEPTIDE (NLE)LFVQRDSKE
    Chains: D
    Engineered: YES
    Other Details: SYNTHETIC PEPTIDE CONTAINING UNNATURAL AMINO ACID NORLEUCINE AT IT'S AMINO TERMINUS
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABD
Biological Unit 1 (1x): ABD
Biological Unit 2 (1x): A  
Biological Unit 3 (1x):  BD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION
2NLE1Mod. Amino AcidNORLEUCINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2NLE1Mod. Amino AcidNORLEUCINE
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2NLE-1Mod. Amino AcidNORLEUCINE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2NLE1Mod. Amino AcidNORLEUCINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:119 , HOH A:146 , HOH A:204 , ASP B:119 , HOH B:144 , HOH B:199BINDING SITE FOR RESIDUE MG A 1

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3G3P)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3G3P)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3G3P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3G3P)

(-) Exons   (0, 0)

(no "Exon" information available for 3G3P)

(-) 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:82
 aligned with CLPS_CAUCR | Q9A5I0 from UniProtKB/Swiss-Prot  Length:119

    Alignment length:82
                                    47        57        67        77        87        97       107       117  
           CLPS_CAUCR    38 PSLYRVLILNDDYTPMEFVVYVLERFFNKSREDATRIMLHVHQNGVGVCGVYTYEVAETKVAQVIDSARRHQHPLQCTMEKD 119
               SCOP domains d3g3pa_ A: automated matches                                                       SCOP domains
               CATH domains 3g3pA00 A:38-119  [code=3.30.1390.10, no name defined]                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhheeeeeeehhhhhhhhhhhhhhhhhhh....eeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------- Transcript
                 3g3p A  38 PSLYRVLILNDDYTPAEFVVYVLERFFNKSREDATRIMLHVHQNGVGVCGVYTYEVAETKVAQVIDSARRHQHPLQCTMEKD 119
                                    47        57        67        77        87        97       107       117  


Chain B from PDB  Type:PROTEIN  Length:82
 aligned with CLPS_CAUCR | Q9A5I0 from UniProtKB/Swiss-Prot  Length:119

    Alignment length:82
                                    47        57        67        77        87        97       107       117  
           CLPS_CAUCR    38 PSLYRVLILNDDYTPMEFVVYVLERFFNKSREDATRIMLHVHQNGVGVCGVYTYEVAETKVAQVIDSARRHQHPLQCTMEKD 119
               SCOP domains d3g3pb_ B: automated matches                                                       SCOP domains
               CATH domains 3g3pB00 B:38-119  [code=3.30.1390.10, no name defined]                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.....hhhhhhhhhhhhh..hhhhhhhhhhhhhhhheeeeeeehhhhhhhhhhhhhhhhhhh....eeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------- Transcript
                 3g3p B  38 PSLYRVLILNDDYTPAEFVVYVLERFFNKSREDATRIMLHVHQNGVGVCGVYTYEVAETKVAQVIDSARRHQHPLQCTMEKD 119
                                    47        57        67        77        87        97       107       117  


Chain D from PDB  Type:PROTEIN  Length:2
                                  
               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
                 3g3p D   1 lL   2
                            | 
                            1-NLE
   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, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3G3P)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (CLPS_CAUCR | Q9A5I0)
biological process
    GO:0030163    protein catabolic process    The chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

 Visualization

(-) Interactive Views

Asymmetric Unit
  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
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NLE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3g3p)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format | Biol. Unit 3 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
  3g3p
    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
  CLPS_CAUCR | Q9A5I0
    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
  CLPS_CAUCR | Q9A5I0
    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
        CLPS_CAUCR | Q9A5I0: 3dnj 3g19 3g1b 3gq0 3gq1 3gw1

(-) Related Entries Specified in the PDB File

3g1b SAME PROTEIN - DIFFERENT PEPTIDE