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(-)Asym./Biol. Unit
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(-) Description

Title :  HUMAN THROMBOPOIETIN NEUTRALIZING ANTIBODY TN1 FAB
 
Authors :  S. Arai, T. Tamada, E. Honjo, Y. Maeda, R. Kuroki
Date :  21 Mar 08  (Deposition) - 24 Mar 09  (Release) - 24 Mar 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.04
Chains :  Asym./Biol. Unit :  H,L
Keywords :  Thrombopoietin, Fab Fragment(Antibody), Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Arai, T. Tamada, E. Honjo, Y. Maeda, R. Kuroki
Structural And Thermodynamic Characteristics Of Human Thrombopoietin Clarified By Tn1-Fab Binding
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MONOCLONAL TN1 FAB LIGHT CHAIN
    Chains: L
    Engineered: YES
    Expression System: MUS MUSCULUS
    Expression System Cell: HYBRIDOMA CELL
    Expression System Common: MOUSE
    Expression System Taxid: 10090
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - MONOCLONAL TN1 FAB HEAVY CHAIN
    Chains: H
    Engineered: YES
    Expression System: MUS MUSCULUS
    Expression System Cell: HYBRIDOMA CELL
    Expression System Common: MOUSE
    Expression System Taxid: 10090
    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 2ZKH)

(-) Sites  (0, 0)

(no "Site" information available for 2ZKH)

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:98
2H:143 -H:198
3L:23 -L:87
4L:133 -L:193

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Ser L:7 -Pro L:8
2Tyr L:93 -Pro L:94
3Tyr L:139 -Pro L:140
4Phe H:149 -Pro H:150
5Glu H:151 -Pro H:152
6Trp H:191 -Pro H:192

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2ZKH)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2ZKH)

(-) Exons   (0, 0)

(no "Exon" information available for 2ZKH)

(-) 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:209
                                                                                                                                                                                                                                                 
               SCOP domains d2zkhh1 H:1-116 Immunoglobulin heavy chain variable domain, VH                                                      d2zkhh2 H:117-216 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma               SCOP domains
               CATH domains 2zkhH01 H:1-116 Immunoglobulins                                                                                     2zkhH02 H:117-205 Immunoglobulins                                                 ----------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhh.eeeeeee...eeeeeeee.hhhhh..eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeee....ee...eeeee........eeeee...eeeeeeeeeee.....eeee.hhh.....ee...eee..eeeeeeeeeee.hhh.....eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zkh H   1 EVKLEESGGGLVQPGGSMKLSCAASGFTFSDAWMDWVRQSPEKGLEWVAEIRSKVNNHAIHYAESVKGRFTVSRDDSKSSVYLQMNSLRAEDTGIYYCSGWSFLYWGQGTLVTVSAAKTTPPSVYPLAPSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPR 216
                                    10        20        30        40        50        60        70        80        90       100       110       120       137       147       157       167       177       187       197       207         
                                                                                                                                                          129|                                                                               
                                                                                                                                                           137                                                                               


Chain L from PDB  Type:PROTEIN  Length:210
                                                                                                                                                                                                                                                  
               SCOP domains d2zkhl1 L:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                 d2zkhl2 L:108-210 Immunoglobulin light chain kappa constant domain, CL-kappa                            SCOP domains
               CATH domains -----------------------------------------------------------------------------------------------------------2zkhL02 L:108-209 Immunoglobulins                                                                     - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2zkh L   1 QVVLTQSPGIMSASPGEKVTITCSASSSVSYMYWFQQKPGTSPKLWIYSTSNLASGVPARFRGSGSGTSYSLTISRMEAEDAATYYCQQRSGYPRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR 210
                                    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)
  - → 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  (4, 4)

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

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2ZKH)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2ZKH)

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Asymmetric/Biological Unit
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  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2zkh)
 
  Sites
(no "Sites" information available for 2zkh)
 
  Cis Peptide Bonds
    Glu H:151 - Pro H:152   [ RasMol ]  
    Phe H:149 - Pro H:150   [ RasMol ]  
    Ser L:7 - Pro L:8   [ RasMol ]  
    Trp H:191 - Pro H:192   [ RasMol ]  
    Tyr L:139 - Pro L:140   [ RasMol ]  
    Tyr L:93 - Pro L:94   [ RasMol ]  
 

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  2zkh
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 Related Entries

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