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(-) Description

Title :  CONVERGENT SOLUTIONS TO VHH DOMAIN STABILIZATION FROM NATURAL AND IN VITRO EVOLUTION
 
Authors :  C. J. Bond, C. Wiesmann, J. C. Marsters, S. S. Sidhu
Date :  26 Feb 04  (Deposition) - 08 Mar 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,D,E
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  D  (1x)
Biol. Unit 4:  E  (1x)
Keywords :  Heavy Chain Variable Domain, Vhh Domain, Immunoglobulin, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. J. Bond, C. Wiesmann, J. C. Marsters, S. S. Sidhu
A Structure-Based Database Of Antibody Variable Domain Diversity.
J. Mol. Biol. V. 348 699 2005
PubMed-ID: 15826665  |  Reference-DOI: 10.1016/J.JMB.2005.02.063

(-) Compounds

Molecule 1 - ANTIBODY RIG
    Chains: A, B, D, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RIG VHH
    Organism Common: LLAMA
    Organism Scientific: LAMA GLAMA
    Organism Taxid: 9844

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABDE
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   D 
Biological Unit 4 (1x):    E

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1SHM)

(-) SS Bonds  (3, 3)

Asymmetric Unit
No.Residues
1B:22 -B:92
2D:22 -D:92
3E:22 -E:92

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1SHM)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1SHM)

(-) 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:118
                                                                                                                                                      
               SCOP domains d1shma_ A: automated matches                                                                                           SCOP domains
               CATH domains 1shmA00 A:2-113 Immunoglobulins                                                                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..eeee....eeeeeeee.......eeeeeee......eeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeee......eeee...eeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 1shm A   2 VQLQESGGGLVQAGGSLRLSCAASGATGSTYDMGWFRQAPGKERESVAAINWGSAGTYYASSVRGRFTISRDNAKKTVYLQMNSLKPEDTAVYTCGAGRIRESWVTWWGQGTQVTVSS 113
                                    11        21        31        41        51 |      60        70        80  |||   87        97|||    105        
                                                                             52A                            82A||             98H||               
                                                                                                             82B|              98I|               
                                                                                                              82C               98J               


Chain B from PDB  Type:PROTEIN  Length:117
                                                                                                                                                     
               SCOP domains d1shmb_ B: automated matches                                                                                          SCOP domains
               CATH domains 1shmB00 B:2-113 Immunoglobulins                                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..eeee....eeeeeeee.......eeeeeee......eeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeeee.....eeee...eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 1shm B   2 VQLQESGGGLVQAGGSLRLSCAASGATGSTYDMGWFRQAPGKERESVAAINWGSAGTYYASSVRGRFTISRDNAKKTVYLQMNSLKPEDTAVYTCGAGRIESWVTWWGQGTQVTVSS 113
                                    11        21        31        41        51 |      60        70        80  |||   87        97||     106       
                                                                             52A                            82A||             98I|               
                                                                                                             82B|              98J               
                                                                                                              82C                                


Chain D from PDB  Type:PROTEIN  Length:113
                                                                                                                                                 
               SCOP domains d1shmd_ D: automated matches                                                                                      SCOP domains
               CATH domains 1shmD00 D:2-113 Immunoglobulins                                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeee....eeeeeee....eeeeeee......eeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeee.....eeee...eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 1shm D   2 VQLQESGGGLVQAGGSLRLSCAASSTYDMGWFRQAPGKERESVAAINWGSAGTYYASSVRGRFTISRDNAKKTVYLQMNSLKPEDTAVYTCGAGRIESWVTWWGQGTQVTVSS 113
                                    11        21   ||   35        45       |54        64        74       82B|       91      |100       110   
                                                  25|                    52A                            82A||             98I|               
                                                   30                                                    82B|              98J               
                                                                                                          82C                                


Chain E from PDB  Type:PROTEIN  Length:118
                                                                                                                                                      
               SCOP domains d1shme_ E: automated matches                                                                                           SCOP domains
               CATH domains 1shmE00 E:2-113 Immunoglobulins                                                                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..eeee....eeeeeeee.......eeeeeee......eeeeeee.....eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeee......eeee...eeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 1shm E   2 VQLQESGGGLVQAGGSLRLSCAASGATGSTYDMGWFRQAPGKERESVAAINWGSAGTYYASSVRGRFTISRDNAKKTVYLQMNSLKPEDTAVYTCGAGRIRESWVTWWGQGTQVTVSS 113
                                    11        21        31        41        51 |      60        70        80  |||   87        97|||    105        
                                                                             52A                            82A||             98H||               
                                                                                                             82B|              98I|               
                                                                                                              82C               98J
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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, 4)

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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

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  1shm
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 Related Entries

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

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(-) Related Entries Specified in the PDB File

1f2x 1hcv 1mel