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(-) Description

Title :  THE STRUCTURE OF A BIVALENT DIABODY
 
Authors :  R. L. Williams
Date :  29 Aug 94  (Deposition) - 31 Mar 95  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,C,E,G
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  E,G  (1x)
Keywords :  Immunoglobulin, Diabody, Single-Chain Fv, Scfv (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  O. Perisic, P. A. Webb, P. Holliger, G. Winter, R. L. Williams
Crystal Structure Of A Diabody, A Bivalent Antibody Fragment.
Structure V. 2 1217 1994
PubMed-ID: 7704531  |  Reference-DOI: 10.1016/S0969-2126(94)00123-5
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ANTI-PHOSPHATIDYLINOSITOL SPECIFIC PHOSPHOLIPASE C DIABODY
    Chains: A, C, E, G
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: L5MK16
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ACEG
Biological Unit 1 (1x): AC  
Biological Unit 2 (1x):   EG

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1LMK)

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:22 -A:96
2A:223 -A:293
3C:22 -C:96
4C:223 -C:293
5E:22 -E:96
6E:223 -E:293
7G:22 -G:96
8G:223 -G:293

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Ser A:207 -Pro A:208
2Val A:299 -Pro A:300
3Ser C:207 -Pro C:208
4Val C:299 -Pro C:300
5Ser E:207 -Pro E:208
6Val E:299 -Pro E:300
7Ser G:207 -Pro G:208
8Val G:299 -Pro G:300

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1LMK)

(-) 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:238
                                                                                                                                                                                                                                                                              
               SCOP domains d1lmka1 A:2-127 Immunoglobulin heavy chain variable domain, VH                                                                d1lmka2 A:201-312 Immunoglobulin light chain kappa variable domain, VL-kappa                                     SCOP domains
               CATH domains 1lmkA01 A:2-123 Immunoglobulins                                                                                           1lmkA02 A:124-312 Immunoglobulins                                                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...eee.....eeeeeeee......eeeeeeee.....eeeeeeee....eeee.hhhh..eeeeee....eeeeee...hhhhheeeeeeeeee.........ee...eeeee..........eeee..eeee.....eeeeeee............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee...........eeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1lmk A   2 VQLQQSGTELMKPGRSLKISCKTTGYIFSNYWIEWVKQRPGHGLEWIGKILPGGGSNTYNDKFKGKATFTADTSSNIAYMQLSSLTSEDSAVYYCARGEDYYAYWYVLDYWGQGTTVTVSSGGGGSDIELTQSPLSLPVSLGDQASISCRSSQSLVHSNGNTSLHWYLKKPGQSPKLLIYKVSTRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYFCSQSTHVPFTFGSGTKLELK 312
                                    11        21        31        41        51        61        71        81        91       101       111       121     ||204       214       224       234       244       254       264       274       284       294       304        
                                                                                                                                                       127|                                                                                                               
                                                                                                                                                        201                                                                                                               


Chain C from PDB  Type:PROTEIN  Length:238
                                                                                                                                                                                                                                                                              
               SCOP domains d1lmkc1 C:2-127 Immunoglobulin heavy chain variable domain, VH                                                                d1lmkc2 C:201-312 Immunoglobulin light chain kappa variable domain, VL-kappa                                     SCOP domains
               CATH domains 1lmkC01 C:2-123 Immunoglobulins                                                                                           1lmkC02 C:124-312 Immunoglobulins                                                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............................................................................................................................................................................................................................................. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1lmk C   2 VQLQQSGTELMKPGRSLKISCKTTGYIFSNYWIEWVKQRPGHGLEWIGKILPGGGSNTYNDKFKGKATFTADTSSNIAYMQLSSLTSEDSAVYYCARGEDYYAYWYVLDYWGQGTTVTVSSGGGGSDIELTQSPLSLPVSLGDQASISCRSSQSLVHSNGNTSLHWYLKKPGQSPKLLIYKVSTRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYFCSQSTHVPFTFGSGTKLELK 312
                                    11        21        31        41        51        61        71        81        91       101       111       121     ||204       214       224       234       244       254       264       274       284       294       304        
                                                                                                                                                       127|                                                                                                               
                                                                                                                                                        201                                                                                                               


Chain E from PDB  Type:PROTEIN  Length:238
                                                                                                                                                                                                                                                                              
               SCOP domains d1lmke1 E:2-127 Immunoglobulin heavy chain variable domain, VH                                                                d1lmke2 E:201-312 Immunoglobulin light chain kappa variable domain, VL-kappa                                     SCOP domains
               CATH domains 1lmkE01 E:2-123 Immunoglobulins                                                                                           1lmkE02 E:124-312 Immunoglobulins                                                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...eee.....eeeeeee...hhh.eeeeeeee......eeeeee......eee.hhh...eeeee.....eeeeee...hhhhheeeeeeeeee.........ee...eeeee..........eeee..eeee.....eeeeeee............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1lmk E   2 VQLQQSGTELMKPGRSLKISCKTTGYIFSNYWIEWVKQRPGHGLEWIGKILPGGGSNTYNDKFKGKATFTADTSSNIAYMQLSSLTSEDSAVYYCARGEDYYAYWYVLDYWGQGTTVTVSSGGGGSDIELTQSPLSLPVSLGDQASISCRSSQSLVHSNGNTSLHWYLKKPGQSPKLLIYKVSTRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYFCSQSTHVPFTFGSGTKLELK 312
                                    11        21        31        41        51        61        71        81        91       101       111       121     ||204       214       224       234       244       254       264       274       284       294       304        
                                                                                                                                                       127|                                                                                                               
                                                                                                                                                        201                                                                                                               


Chain G from PDB  Type:PROTEIN  Length:238
                                                                                                                                                                                                                                                                              
               SCOP domains d1lmkg1 G:2-127 Immunoglobulin heavy chain variable domain, VH                                                                d1lmkg2 G:201-312 Immunoglobulin light chain kappa variable domain, VL-kappa                                     SCOP domains
               CATH domains 1lmkG01 G:2-123 Immunoglobulins                                                                                           1lmkG02 G:124-312 Immunoglobulins                                                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............................................................................................................................................................................................................................................. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1lmk G   2 VQLQQSGTELMKPGRSLKISCKTTGYIFSNYWIEWVKQRPGHGLEWIGKILPGGGSNTYNDKFKGKATFTADTSSNIAYMQLSSLTSEDSAVYYCARGEDYYAYWYVLDYWGQGTTVTVSSGGGGSDIELTQSPLSLPVSLGDQASISCRSSQSLVHSNGNTSLHWYLKKPGQSPKLLIYKVSTRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYFCSQSTHVPFTFGSGTKLELK 312
                                    11        21        31        41        51        61        71        81        91       101       111       121     ||204       214       224       234       244       254       264       274       284       294       304        
                                                                                                                                                       127|                                                                                                               
                                                                                                                                                        201
   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  (2, 8)

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

(-) CATH Domains  (1, 8)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)
(-)
Architecture: Sandwich (5577)
(-)
Topology: Immunoglobulin-like (3897)
(-)
Homologous Superfamily: Immunoglobulins (2282)
(-)
House mouse (Mus musculus) (616)
1a1lmkA01A:2-123
1b1lmkA02A:124-312
1c1lmkC02C:124-312
1d1lmkE02E:124-312
1e1lmkG02G:124-312
1f1lmkC01C:2-123
1g1lmkE01E:2-123
1h1lmkG01G:2-123

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

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  Sites
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  Cis Peptide Bonds
    Ser A:207 - Pro A:208   [ RasMol ]  
    Ser C:207 - Pro C:208   [ RasMol ]  
    Ser E:207 - Pro E:208   [ RasMol ]  
    Ser G:207 - Pro G:208   [ RasMol ]  
    Val A:299 - Pro A:300   [ RasMol ]  
    Val C:299 - Pro C:300   [ RasMol ]  
    Val E:299 - Pro E:300   [ RasMol ]  
    Val G:299 - Pro G:300   [ RasMol ]  
 
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