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(-) Description

Title :  IMMUNOGLOBULIN LIGHT CHAIN PROTEIN
 
Authors :  N. Schormann, M. D. Benson
Date :  19 Jul 95  (Deposition) - 15 Oct 95  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C,D,E,F  (2x)
Keywords :  Immunoglobulin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Schormann, J. R. Murrell, J. J. Liepnieks, M. D. Benson
Tertiary Structure Of An Amyloid Immunoglobulin Light Chain Protein: A Proposed Model For Amyloid Fibril Formation.
Proc. Natl. Acad. Sci. Usa V. 92 9490 1995
PubMed-ID: 7568160  |  Reference-DOI: 10.1073/PNAS.92.21.9490
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BENCE-JONES KAPPA I PROTEIN BRE
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Gene: CDNA (GENBANK ACCESSION CODE U31344)
    Expression System Plasmid: PCZ11
    Expression System Strain: HB101
    Expression System Taxid: 562
    Gene: CDNA (GENBANK ACCESSION CODE
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: PATIENT BRE
    Synonym: BENCE-JONES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (2x): ABCDEF

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1BRE)

(-) Sites  (0, 0)

(no "Site" information available for 1BRE)

(-) SS Bonds  (6, 6)

Asymmetric Unit
No.Residues
1A:23 -A:88
2B:23 -B:88
3C:23 -C:88
4D:23 -D:88
5E:23 -E:88
6F:23 -F:88

(-) Cis Peptide Bonds  (12, 12)

Asymmetric Unit
No.Residues
1Ser A:7 -Pro A:8
2Leu A:94 -Pro A:95
3Ser B:7 -Pro B:8
4Leu B:94 -Pro B:95
5Ser C:7 -Pro C:8
6Leu C:94 -Pro C:95
7Ser D:7 -Pro D:8
8Leu D:94 -Pro D:95
9Ser E:7 -Pro E:8
10Leu E:94 -Pro E:95
11Ser F:7 -Pro F:8
12Leu F:94 -Pro F:95

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1BRE)

(-) 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:107
                                                                                                                                           
               SCOP domains d1brea_ A: Immunoglobulin light chain kappa variable domain, VL-kappa                                       SCOP domains
               CATH domains 1breA00 A:1-107 Immunoglobulins                                                                             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeee.......eeee.............eeeeee..eeeeee....hhh.eeeeeee...........eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 1bre A   1 DIQMTQSPSSLSASVGDRVTITCQASQDISDYLIWYQQKLGKAPNLLIYDASTLETGVPSRFSGSGSGTEYTFTISSLQPEDIATYYCQQYDDLPYTFGQGTKVEIK 107
                                    10        20        30        40        50        60        70        80        90       100       


Chain B from PDB  Type:PROTEIN  Length:107
                                                                                                                                           
               SCOP domains d1breb_ B: Immunoglobulin light chain kappa variable domain, VL-kappa                                       SCOP domains
               CATH domains 1breB00 B:1-107 Immunoglobulins                                                                             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee........eeeee......eeee.............eeee....eeeeee....hhh..eeeee.............eeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 1bre B   1 DIQMTQSPSSLSASVGDRVTITCQASQDISDYLIWYQQKLGKAPNLLIYDASTLETGVPSRFSGSGSGTEYTFTISSLQPEDIATYYCQQYDDLPYTFGQGTKVEIK 107
                                    10        20        30        40        50        60        70        80        90       100       


Chain C from PDB  Type:PROTEIN  Length:107
                                                                                                                                           
               SCOP domains d1brec_ C: Immunoglobulin light chain kappa variable domain, VL-kappa                                       SCOP domains
               CATH domains 1breC00 C:1-107 Immunoglobulins                                                                             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..........eeeeeeee........eeeee......eeeee............eeeeee..eeeeeee...hhh.eeeee.............eee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 1bre C   1 DIQMTQSPSSLSASVGDRVTITCQASQDISDYLIWYQQKLGKAPNLLIYDASTLETGVPSRFSGSGSGTEYTFTISSLQPEDIATYYCQQYDDLPYTFGQGTKVEIK 107
                                    10        20        30        40        50        60        70        80        90       100       


Chain D from PDB  Type:PROTEIN  Length:107
                                                                                                                                           
               SCOP domains d1bred_ D: Immunoglobulin light chain kappa variable domain, VL-kappa                                       SCOP domains
               CATH domains 1breD00 D:1-107 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
                 1bre D   1 DIQMTQSPSSLSASVGDRVTITCQASQDISDYLIWYQQKLGKAPNLLIYDASTLETGVPSRFSGSGSGTEYTFTISSLQPEDIATYYCQQYDDLPYTFGQGTKVEIK 107
                                    10        20        30        40        50        60        70        80        90       100       


Chain E from PDB  Type:PROTEIN  Length:107
                                                                                                                                           
               SCOP domains d1bree_ E: Immunoglobulin light chain kappa variable domain, VL-kappa                                       SCOP domains
               CATH domains 1breE00 E:1-107 Immunoglobulins                                                                             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eee......eeeeeee.......eeeeee......eeeee............eeeeee..eeeeee....hhh..eeeeee............eee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 1bre E   1 DIQMTQSPSSLSASVGDRVTITCQASQDISDYLIWYQQKLGKAPNLLIYDASTLETGVPSRFSGSGSGTEYTFTISSLQPEDIATYYCQQYDDLPYTFGQGTKVEIK 107
                                    10        20        30        40        50        60        70        80        90       100       


Chain F from PDB  Type:PROTEIN  Length:107
                                                                                                                                           
               SCOP domains d1bref_ F: Immunoglobulin light chain kappa variable domain, VL-kappa                                       SCOP domains
               CATH domains 1breF00 F:1-107 Immunoglobulins                                                                             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..eeeee....eeeeee........eeeeee.......eeee............eeeee...eeeeee........eeeeeee...........eeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 1bre F   1 DIQMTQSPSSLSASVGDRVTITCQASQDISDYLIWYQQKLGKAPNLLIYDASTLETGVPSRFSGSGSGTEYTFTISSLQPEDIATYYCQQYDDLPYTFGQGTKVEIK 107
                                    10        20        30        40        50        60        70        80        90       100
   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, 6)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 6)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)
(-)
Architecture: Sandwich (5577)
(-)
Topology: Immunoglobulin-like (3897)
(-)
Homologous Superfamily: Immunoglobulins (2282)
(-)
Human (Homo sapiens) (912)
1a1breA00A:1-107
1b1breB00B:1-107
1c1breC00C:1-107
1d1breD00D:1-107
1e1breE00E:1-107
1f1breF00F:1-107

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1BRE)

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  Cis Peptide Bonds
    Leu A:94 - Pro A:95   [ RasMol ]  
    Leu B:94 - Pro B:95   [ RasMol ]  
    Leu C:94 - Pro C:95   [ RasMol ]  
    Leu D:94 - Pro D:95   [ RasMol ]  
    Leu E:94 - Pro E:95   [ RasMol ]  
    Leu F:94 - Pro F:95   [ RasMol ]  
    Ser A:7 - Pro A:8   [ RasMol ]  
    Ser B:7 - Pro B:8   [ RasMol ]  
    Ser C:7 - Pro C:8   [ RasMol ]  
    Ser D:7 - Pro D:8   [ RasMol ]  
    Ser E:7 - Pro E:8   [ RasMol ]  
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