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

(-) Description

Title :  X-RAY CRYSTAL STRUCTURE OF CHEMICALLY SYNTHESIZED CRAMBIN
 
Authors :  D. Bang, V. Tereshko, A. A. Kossiakoff, S. B. Kent
Date :  13 Dec 05  (Deposition) - 16 Jan 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A
Keywords :  Crambin, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Bang, V. Tereshko, A. A. Kossiakoff, S. B. Kent
Role Of A Salt Bridge In The Model Protein Crambin Explored By Chemical Protein Synthesis: X-Ray Structure Of A Unique Protein Analogue, [V15A]Crambin-Alpha-Carboxamide.
Mol Biosyst V. 5 750 2009
PubMed-ID: 19562114  |  Reference-DOI: 10.1039/B903610E

(-) Compounds

Molecule 1 - CRAMBIN
    Chains: A
    Engineered: YES
    Other Details: THE PROTEIN WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE PROTEIN CAN BE NATURALLY FOUND IN CRAMBE ABYSSINICA (ABYSSINIAN CRAMBE).
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2FD7)

(-) Sites  (0, 0)

(no "Site" information available for 2FD7)

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:3 -A:40
2A:4 -A:32
3A:16 -A:26

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2FD7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric/Biological Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_CRAM_CRAAB_001 *P22SCRAM_CRAAB  ---  ---AP22S
2UniProtVAR_CRAM_CRAAB_002 *L25ICRAM_CRAAB  ---  ---AL25I
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIONINPS00271 Plant thionins signature.CRAM_CRAAB3-16  1A:3-16

(-) Exons   (0, 0)

(no "Exon" information available for 2FD7)

(-) Sequences/Alignments

Asymmetric/Biological 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:46
 aligned with CRAM_CRAAB | P01542 from UniProtKB/Swiss-Prot  Length:46

    Alignment length:46
                                    10        20        30        40      
            CRAM_CRAAB    1 TTCCPSIVARSNFNVCRLPGTPEALCATYTGCIIIPGATCPGDYAN 46
               SCOP domains d2fd7a1 A:1-46 Crambin                         SCOP domains
               CATH domains 2fd7A00 A:1-46                                 CATH domains
               Pfam domains ---------------------------------------------- Pfam domains
         Sec.struct. author .ee..hhhhhhhhhhhhh...hhhhhhhhhh.ee......hhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------S--I--------------------- SAPs(SNPs)
                    PROSITE --THIONIN       ------------------------------ PROSITE
                 Transcript ---------------------------------------------- Transcript
                  2fd7 A  1 TTCCPSIVARSNFNVCRLPGTPEALCATYTGCIIIPGATCPGDYAN 46
                                    10        20        30        40
   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)

Asymmetric/Biological Unit
(-)
Class: Small proteins (3458)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2FD7)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CRAM_CRAAB | P01542)
biological process
    GO:0006952    defense response    Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
(no "Ligands, Modified Residues, Ions" information available for 2fd7)
 
  Sites
(no "Sites" information available for 2fd7)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2fd7)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit 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
  2fd7
    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
  CRAM_CRAAB | P01542
    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
  CRAM_CRAAB | P01542
    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
        CRAM_CRAAB | P01542: 1ab1 1cbn 1ccm 1ccn 1cnr 1crn 1cxr 1ejg 1jxt 1jxu 1jxw 1jxx 1jxy 1yv8 1yva 2eya 2eyb 2eyc 2eyd 2fd9 3nir 3u7t 3ue7 4fc1

(-) Related Entries Specified in the PDB File

2fd9