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(-) Description

Title :  CRYSTAL STRUCTURE OF FAB D3H44
 
Authors :  K. Faelber, D. Kirchhofer, L. Presta, R. F. Kelley, Y. A. Muller
Date :  03 Aug 01  (Deposition) - 03 Feb 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  H,L
Keywords :  Antigen-Antibody Recognition, Humanized Antibody, Blood Coagulation, Crystal Structure, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Faelber, D. Kirchhofer, L. Presta, R. F. Kelley, Y. A. Muller
The 1. 85 A Resolution Crystal Structures Of Tissue Factor In Complex With Humanized Fab D3H44 And Of Free Humanized Fab D3H44: Revisiting The Solvation Of Antigen Combining Sites.
J. Mol. Biol. V. 313 83 2001
PubMed-ID: 11601848  |  Reference-DOI: 10.1006/JMBI.2001.5036
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - IMMUNOGLOBULIN FAB D3H44, LIGHT CHAIN
    Chains: L
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PEMX1
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: FAB FRAGMENT
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - IMMUNOGLOBULIN FAB D3H44, HEAVY CHAIN
    Chains: H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PEMX1
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: FAB FRAGMENT
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : HL

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1JPT)

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:96
2H:144 -H:200
3L:23 -L:88
4L:134 -L:194

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Ser L:7 -Pro L:8
2Ser L:94 -Pro L:95
3Tyr L:140 -Pro L:141
4Phe H:150 -Pro H:151
5Glu H:152 -Pro H:153

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1JPT)

(-) 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 H from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                    
               SCOP domains d1jpth1 H:1-117 Immunoglobulin heavy chain variable domain, VH                                                       d1jpth2 H:118-217 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                 SCOP domains
               CATH domains 1jptH01 H:1-117 Immunoglobulins                                                                                      1jptH02 H:118-216 Immunoglobulins                                                             - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhheeeeeee.....eeeeeee......eee.......eeeeeehhh.eeeeee...hhhhheeeeeeee....eeee...eeeee........eeeee.....eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhhhh..eeeeeeehhhheeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jpt H   1 EVQLVESGGGLVQPGGSLRLSCAASGFNIKEYYMHWVRQAPGKGLEWVGLIDPEQGNTIYDPKFQDRATISADNSKNTAYLQMNSLRAEDTAVYYCARDTAAYFDYWGQGTLVTVSSASTKGPSVFPLAPSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP 217
                                    10        20        30        40        50        60        70        80        90       100       110       120       130||     145       155       165       175       185       195       205       215  
                                                                                                                                                            131|                                                                                
                                                                                                                                                             137                                                                                


Chain L from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains d1jptl1 L:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                 d1jptl2 L:108-213 Immunoglobulin light chain kappa constant domain, CL-kappa                               SCOP domains
               CATH domains 1jptL01 L:1-108 Immunoglobulins                                                                             1jptL02 L:109-211 Immunoglobulins                                                                      -- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeeee......eeeee....hhhhh.eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhhh.eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jpt L   1 DIQMTQSPSSLSASVGDRVTITCRASRDIKSYLNWYQQKPGKAPKVLIYYATSLAEGVPSRFSGSGSGTDYTLTISSLQPEDFATYYCLQHGESPWTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE 213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
   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  (4, 4)

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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

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  Cis Peptide Bonds
    Glu H:152 - Pro H:153   [ RasMol ]  
    Phe H:150 - Pro H:151   [ RasMol ]  
    Ser L:7 - Pro L:8   [ RasMol ]  
    Ser L:94 - Pro L:95   [ RasMol ]  
    Tyr L:140 - Pro L:141   [ RasMol ]  
 

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 Related Entries

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(-) Related Entries Specified in the PDB File

1jps 1JPS CONTAINS TISSUE FACTOR COMPLEXED WITH HUMANIZED FAB D3H44