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(-) Description

Title :  CRYSTAL STRUCTURE OF FABOX117
 
Authors :  J. E. Nettleship, J. Ren, R. J. Owens, Oxford Protein Production Facility (Oppf)
Date :  20 Jun 08  (Deposition) - 12 Aug 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Antibody Fragments, Fabs, Transient Expression, Structural Genomics, Oxford Protein Production Facility, Oppf, Immunoglobulin Domain, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. E. Nettleship, J. Ren, N. Rahman, N. S. Berrow, D. Hatherley, A. N. Barclay, R. J. Owens
A Pipeline For The Production Of Antibody Fragments For Structural Studies Using Transient Expression In Hek 293T Cells.
Protein Expr. Purif. V. 62 83 2008
PubMed-ID: 18662785  |  Reference-DOI: 10.1016/J.PEP.2008.06.017
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FABOX117 LIGHT CHAIN FRAGMENT
    Chains: A, C
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Organ: HUMAN EMBRYONIC KIDNEY CELLS
    Expression System Plasmid: POPINVL
    Expression System Strain: 293T
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - FABOX117 HEAVY CHAIN FRAGMENT
    Chains: B, D
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Organ: HUMAN EMBRYONIC KIDNEY CELLS
    Expression System Plasmid: POPINVH
    Expression System Strain: 293T
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3DIF)

(-) Sites  (0, 0)

(no "Site" information available for 3DIF)

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:23 -A:88
2A:134 -A:194
3B:22 -B:96
4B:146 -B:201
5C:23 -C:88
6C:134 -C:194
7D:22 -D:96
8D:146 -D:201

(-) Cis Peptide Bonds  (12, 12)

Asymmetric Unit
No.Residues
1Ser A:7 -Pro A:8
2Thr A:94 -Pro A:95
3Tyr A:140 -Pro A:141
4Phe B:152 -Pro B:153
5Glu B:154 -Pro B:155
6Trp B:194 -Pro B:195
7Ser C:7 -Pro C:8
8Thr C:94 -Pro C:95
9Tyr C:140 -Pro C:141
10Phe D:152 -Pro D:153
11Glu D:154 -Pro D:155
12Trp D:194 -Pro D:195

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3DIF)

(-) 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:213
                                                                                                                                                                                                                                                     
               SCOP domains d3difa1 A:1-107 automated matches                                                                          d3difa2 A:108-213 automated matches                                                                        SCOP domains
               CATH domains 3difA01 A:1-108 Immunoglobulins                                                                             3difA02 A:109-211 Immunoglobulins                                                                      -- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee...........eeeeee......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhhh.eeeeeeee..eeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dif A   1 DIVITQSPKFMSTSVGDRVSITCKASQDVSTAVAWFQQKPGQSPKLLIYSASYRYTGVPDRFTGSGSGTDFTFTISSVQAEDLAVYYCQQHYSTPWTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE 213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210   


Chain B from PDB  Type:PROTEIN  Length:211
                                                                                                                                                                                                                                                   
               SCOP domains -----------------------------------------------------------------------------------------------------------------------d3difb1 B:120-218 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma              SCOP domains
               CATH domains 3difB01 B:1-119 Immunoglobulins                                                                                        3difB02 B:120-216 Immunoglobulins                                                         -- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeeee...eeeeeeeee....eeee.hhhh..eeeeee....eeeeee...hhhhheeeeeee.........ee...eeeee........eeeee...eeeeeeeeeee.....eeee........eee...eee..eeeeeeeeeee.........eeeeee....eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dif B   1 EVKLQQSGPELVKPGASVKISCKASGYSFTSYYIHWVKQRPGQGLEWIGWVFPGSGNTKYNEKFKGKATLTADTSSSTAYMQLSSLTSEDSAVYFCARGNYDRAWFAYWGQGTLVTVSAAKTTPPSVYPLAPSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVP 218
                                    10        20        30        40        50        60        70        80        90       100       110       120       130 ||    147       157       167       177       187       197       207       217 
                                                                                                                                                             132|                                                                              
                                                                                                                                                              140                                                                              


Chain C from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                      
               SCOP domains d3difc1 C:1-107 automated matches                                                                          d3difc2 C:108-214 automated matches                                                                         SCOP domains
               CATH domains 3difC01 C:1-108 Immunoglobulins                                                                             3difC02 C:109-211 Immunoglobulins                                                                      --- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee...........eeeeee......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhhh.eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dif C   1 DIVITQSPKFMSTSVGDRVSITCKASQDVSTAVAWFQQKPGQSPKLLIYSASYRYTGVPDRFTGSGSGTDFTFTISSVQAEDLAVYYCQQHYSTPWTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC 214
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210    


Chain D from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains -----------------------------------------------------------------------------------------------------------------------d3difd1 D:120-218 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma             -- SCOP domains
               CATH domains 3difD01 D:1-119 Immunoglobulins                                                                                        3difD02 D:120-216 Immunoglobulins                                                         ---- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeeee...eeeeeeeee....eeee.hhhh..eeeeee....eeeeee...hhhhheeeeeee.........ee...eeeee........eeeee...eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.........eeeeee....eeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dif D   1 EVKLQQSGPELVKPGASVKISCKASGYSFTSYYIHWVKQRPGQGLEWIGWVFPGSGNTKYNEKFKGKATLTADTSSSTAYMQLSSLTSEDSAVYFCARGNYDRAWFAYWGQGTLVTVSAAKTTPPSVYPLAPSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRD 220
                                    10        20        30        40        50        60        70        80        90       100       110       120       130 ||    147       157       167       177       187       197       207       217   
                                                                                                                                                             132|                                                                                
                                                                                                                                                              140
   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  (3, 6)

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)
(-)
Homo sapiens. Organism_taxid: 9606. (14)
1a3difA02A:109-211
1b3difC02C:109-211
1c3difA01A:1-108
1d3difC01C:1-108
1e3difB01B:1-119
1f3difD01D:1-119
1g3difB02B:120-216
1h3difD02D:120-216

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3DIF)

(-) Gene Ontology  (0, 0)

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

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  Cis Peptide Bonds
    Glu B:154 - Pro B:155   [ RasMol ]  
    Glu D:154 - Pro D:155   [ RasMol ]  
    Phe B:152 - Pro B:153   [ RasMol ]  
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    Thr A:94 - Pro A:95   [ RasMol ]  
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    Trp B:194 - Pro B:195   [ RasMol ]  
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3dgg CRYSTAL STRUCTURE OF FABOX108