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 :  LEN K30T MUTANT: A DOMAIN FLIP AS A RESULT OF A SINGLE AMINO ACID SUBSTITUTION
 
Authors :  M. Schiffer, P. R. Pokkuluri
Date :  12 May 98  (Deposition) - 18 May 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Immunoglobulin, Kappa-Iv, Light Chain Dimer (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. R. Pokkuluri, D. B. Huang, R. Raffen, X. Cai, G. Johnson, P. W. Stevens, F. J. Stevens, M. Schiffer
A Domain Flip As A Result Of A Single Amino-Acid Substitution.
Structure V. 6 1067 1998
PubMed-ID: 9739086  |  Reference-DOI: 10.1016/S0969-2126(98)00107-5
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LEN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: JM83
    Expression System Taxid: 562
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: KAPPA-IV LIGHT CHAIN DIMER

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4LVE)

(-) Sites  (0, 0)

(no "Site" information available for 4LVE)

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:23 -A:88
2B:323 -B:388

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Ser A:7 -Pro A:8
2Thr A:94 -Pro A:95
3Ser B:307 -Pro B:308
4Thr B:394 -Pro B:395

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4LVE)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4LVE)

(-) Exons   (0, 0)

(no "Exon" information available for 4LVE)

(-) 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:114
                                                                                                                                                   
               SCOP domains d4lvea_ A: Immunoglobulin light chain kappa variable domain, VL-kappa                                              SCOP domains
               CATH domains 4lveA00 A:1-108 Immunoglobulins                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.............eeeeee......eeeee............eeeeee..eeeeee....hhh.eeeeeee...........eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                4lve A    1 DIVMTQSPDSLAVSLGERATINCKSSQSVLYSSNSTNYLAWYQQKPGQPPKLLIYWASTRESGVPDRFSGSGSGTDFTLTISSLQAEDVAVYYCQQYYSTPYSFGQGTKLEIKR  108
                                    10        20       27C|||     34        44        54        64        74        84        94       104    
                                                     27A|||||                                                                                 
                                                      27B||||                                                                                 
                                                       27C|||                                                                                 
                                                        27D||                                                                                 
                                                         27E|                                                                                 
                                                          27F                                                                                 


Chain B from PDB  Type:PROTEIN  Length:113
                                                                                                                                                  
               SCOP domains d4lveb_ B: Immunoglobulin light chain kappa variable domain, VL-kappa                                             SCOP domains
               CATH domains 4lveB00 B:301-407 Immunoglobulins                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.............eeeeee......eeee.............eeeeee..eeeeee....hhh.eeeeeee...........eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                4lve B  301 DIVMTQSPDSLAVSLGERATINCKSSQSVLYSSNSTNYLAWYQQKPGQPPKLLIYWASTRESGVPDRFSGSGSGTDFTLTISSLQAEDVAVYYCQQYYSTPYSFGQGTKLEIK  407
                                   310       320      327C|||    334       344       354       364       374       384       394       404   
                                                    327A|||||                                                                                
                                                     327B||||                                                                                
                                                      327C|||                                                                                
                                                       327D||                                                                                
                                                        327E|                                                                                
                                                         327F
   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/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4LVE)

(-) Gene Ontology  (14, 27)

Asymmetric/Biological Unit(hide GO term definitions)

 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 4lve)
 
  Sites
(no "Sites" information available for 4lve)
 
  Cis Peptide Bonds
    Ser A:7 - Pro A:8   [ RasMol ]  
    Ser B:307 - Pro B:308   [ RasMol ]  
    Thr A:94 - Pro A:95   [ RasMol ]  
    Thr B:394 - Pro B:395   [ RasMol ]  
 

(-) 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
  4lve
    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
  KV401_HUMAN | P06312
    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
  KV401_HUMAN | P06312
    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
        KV401_HUMAN | P06312: 1dh6 1eeq 1eeu 1efq 1ek3 1lve 1qac 2lve 3lve 5lve

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4LVE)