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(-) Description

Title :  CRYSTAL STRUCTURE OF SAG506-01, TETRAGONAL, CRYSTAL 1
 
Authors :  C. L. Brooks, R. J. Blackler, S. Gerstenbruch, P. Kosma, S. Muller- Loennies, H. Brade, S. V. Evans
Date :  18 Jul 08  (Deposition) - 02 Dec 08  (Release) - 02 Dec 08  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Antibody, Kdo, Twinning, Pseudo-Symmetry, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. L. Brooks, R. J. Blackler, S. Gerstenbruch, P. Kosma, S. Muller-Loennies, H. Brade, S. V. Evans
Pseudo-Symmetry And Twinning In Crystals Of Homologous Antibody Fv Fragments.
Acta Crystallogr. , Sect. D V. 64 1250 2008
PubMed-ID: 19018101  |  Reference-DOI: 10.1107/S0907444908033453
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ANTIBODY FV FRAGMENT SAG506-01
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSFJ8
    Expression System Strain: TG1
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: VARIABLE REGION FRAGMENT (FV)
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 2 - IG-LIKE PROTEIN
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1KDO1Ligand/Ion3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACID
2MG1Ligand/IonMAGNESIUM ION
3PG41Ligand/IonTETRAETHYLENE GLYCOL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:27D , SER A:91 , TYR A:92 , ARG A:95 , TYR B:33 , PHE B:50 , ARG B:52 , ASP B:100 , HOH B:119 , HOH B:125BINDING SITE FOR RESIDUE KDO B 114
2AC2SOFTWAREGLU A:55 , HOH A:136 , HOH A:174 , HOH A:189 , ASP B:101BINDING SITE FOR RESIDUE MG A 115
3AC3SOFTWAREPRO A:40 , GLY A:41 , ALA B:52C , LYS B:53 , TYR B:97BINDING SITE FOR RESIDUE PG4 B 116

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:23 -A:88
2B:22 -B:92

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ser A:7 -Pro A:8

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3DV4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3DV4)

(-) Exons   (0, 0)

(no "Exon" information available for 3DV4)

(-) 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:112
 aligned with A0N262_MOUSE | A0N262 from UniProtKB/TrEMBL  Length:115

    Alignment length:112
                                                                                                                            98              
                                                                                                                          97 |              
                                    11        21        31        41        51        61        71        81        91     | 100       110  
        A0N262_MOUSE      2 DIQLTQSPSSLAVSAGEKVTMSCKSSQSVLYSSNQKNYLAWYQQKPGQSPKLLIYWASTRESGVPDRFTGSGSGTDFTLTISSVQAEDLAVYYCHQ-YLSHTFGGGTKLEIK  112
               SCOP domains d3dv4a_ A: automated matches                                                                                     SCOP domains
               CATH domains 3dv4A00 A:1-106 Immunoglobulins                                                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee....ee....ee.eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee.....ee...eeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                3dv4 A    1 DIVLTQSPSSLAVSAGERVTMSCKSSQSLFKSRNQKNYLAWYQQKPGQSPKLLIYWASTRESGVPDRFTGSGSGTDFTLTINGVQAEDLAVYYCKQSYNLRTFGGGTKLELK  106
                                    10        20       27C|||     34        44        54        64        74        84        94       104  
                                                     27A|||||                                                                               
                                                      27B||||                                                                               
                                                       27C|||                                                                               
                                                        27D||                                                                               
                                                         27E|                                                                               
                                                          27F                                                                               


Chain B from PDB  Type:PROTEIN  Length:119
 aligned with A2NU21_MOUSE | A2NU21 from UniProtKB/TrEMBL  Length:119

    Alignment length:121
                                                                                                                              119                    
                                    28        38        48        58        68        78        88        98       108       118|        -         - 
        A2NU21_MOUSE     19 EVKLVESGGGLVQPGGSLSLSCAASGFTFTDYYMSWVRQLPGKALEWLGFIRNKANGYTTEYSASVKGRFTISRDNSQSILYLQMNALRAEDSATYYCAKD--------------------    -
               SCOP domains d3dv4b_ B: automated matches                                                                                              SCOP domains
               CATH domains 3dv4B00 B:1-113 Immunoglobulins                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhheeeeeee......eeeeee........eee.......eeeeee....eeeeee..--....eeeeeeee........ee...eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                3dv4 B    1 EVKLVESGGGLVQPGGSLRLSCATSGFTFTDYYMSWVRQPPGKALEWLGFIRNKAKGYTVEYSASVKGRFTISRDNSQSILYLQMNT--AEDSATYYCARDGYYVDAMDYWGQGTSVTVSS  113
                                    10        20        30        40        50  |||   57        67        77     || 84        94      |102       112 
                                                                              52A||                            82A| 84             100A|             
                                                                               52B|                             82B                 100B             
                                                                                52C
   Legend:   → Mismatch (orange background)
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  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 3DV4)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3DV4)

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  3dv4
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  A2NU21_MOUSE | A2NU21
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        A0N262_MOUSE | A0N262: 3dus 3duu 3dv6
        A2NU21_MOUSE | A2NU21: 2r1w 2r1x 2r1y 3dur 3dus 3duu 3dv6

(-) Related Entries Specified in the PDB File

3dur 3dus 3duu 3dv6