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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN ANTI POLYHYDROXYBUTYRATE ANTIBODY FV
 
Authors :  H. Watanabe
Date :  29 Nov 05  (Deposition) - 12 Dec 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  H,L
Keywords :  Antibody, Plastic, Polyhydroxybutyrate, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Watanabe, K. Tsumoto, S. Taguchi, K. Yamashita, Y. Doi, Y. Nishimiya, H. Kondo, M. Umetsu, I. Kumagai
A Human Antibody Fragment With High Affinity For The Biodegradable Polymer Film
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ANTI POLYHYDROXYBUTYRATE ANTIBODY FV, HEAVY CHAIN
    Chains: H
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PRA2
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 1-133
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - ANTI POLYHYDROXYBUTYRATE ANTIBODY FV, LIGHT CHAIN
    Chains: L
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PRA2
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 1-110
    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 2D7T)

(-) Sites  (0, 0)

(no "Site" information available for 2D7T)

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:96
2L:23 -L:88

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ser L:7 -Pro L:8
2Tyr L:94 -Pro L:95

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2D7T)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2D7T)

(-) Exons   (0, 0)

(no "Exon" information available for 2D7T)

(-) 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:116
 aligned with Q9UL95_HUMAN | Q9UL95 from UniProtKB/TrEMBL  Length:125

    Alignment length:125
                                    10        20        30        40        50        60        70        80        90       100       110       120     
         Q9UL95_HUMAN     1 EVQLVESGAEVKKPGASVKVSCKASGYTFTGYYMHWVRQAPGQGLEWMGWINPNSGGTNYAQKVQGRVTMTRDTTISTAYMELSRLRSDDTAVYYCARSQGGGRIAAAGDAFDIWGQGTMVTVSS 125
               SCOP domains d2d7th_ H: automated matches                                                                                                  SCOP domains
               CATH domains 2d7tH00 H:1-116 Immunoglobulins                                                                                               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeee......eeeeee......eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeee....---------..ee...eeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 2d7t H   1 QVQLVQSGAEVKKPGASVKVSCKASGYTFTGNYMHWVRQAPGQGLEYMGWINPKSGDTNYAQKFQGRVTMTRDTSISTVYMEVRRLRSDDTAVYYCATGWWG---------MDVWGQGTLVTVSS 116
                                    10        20        30        40        50        60        70        80        90       100 |       - |     111     
                                                                                                                               102       103             


Chain L from PDB  Type:PROTEIN  Length:110
 aligned with Q6GMX0_HUMAN | Q6GMX0 from UniProtKB/TrEMBL  Length:236

    Alignment length:112
                                    32        42        52        62        72        82        92       102       112       122       132  
         Q6GMX0_HUMAN    23 DIQMTQSPSSLSASVGDRVTITCRASQNINNYLNWYQLKPGKAPNLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLRPDDFATYYCQQSYNIPLTFGGGTNVEIKRTVAA 134
               SCOP domains d2d7tl_ L: automated matches                                                                                     SCOP domains
               CATH domains 2d7tL00 L:1-110 Immunoglobulins                                                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee..--.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 2d7t L   1 DIVMTQSPSSLSASVGDRVTITCRASQNINNYLHWYQHEPGKAPKLLIYAASNLQGGVTSRFSGSGSGTDFTLTISTLQPEDFATYYCLQTHAYPLTFGGGTKVDIKR--AA 110
                                    10        20        30        40        50        60        70        80        90       100       | -| 
                                                                                                                                     108  | 
                                                                                                                                        109
   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, 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 2D7T)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2D7T)

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(no "Sites" information available for 2d7t)
 
  Cis Peptide Bonds
    Ser L:7 - Pro L:8   [ RasMol ]  
    Tyr L:94 - Pro L:95   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        Q6GMX0_HUMAN | Q6GMX0: 5vob 5voc
UniProtKB/TrEMBL
        Q6GMX0_HUMAN | Q6GMX0: 1bey

(-) Related Entries Specified in the PDB File

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