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(-) Description

Title :  THREE-DIMENSIONAL STRUCTURE OF ANTI-AMPICILLIN SINGLE CHAIN FV FRAGMENT COMPLEXED WITH THE HAPTEN.
 
Authors :  J. Burmester, S. Spinelli, L. Pugliese, A. Krebber, A. Honegger, S. Jun B. Schimmele, C. Cambillau, A. Pluckthun
Date :  15 Feb 01  (Deposition) - 02 Aug 01  (Release) - 29 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Anti-Ampicillin Antibodies (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Burmester, S. Spinelli, L. Pugliese, A. Krebber, A. Honegger, S. Jung, B. Schimmele, C. Cambillau, A. Pluckthun
Selection, Characterization And X-Ray Structure Of Anti-Ampicillin Single-Chain Fv Fragments From Phage-Displayed Murine Antibody Libraries
J. Mol. Biol. V. 309 671 2001
PubMed-ID: 11397088  |  Reference-DOI: 10.1006/JMBI.2001.4663

(-) Compounds

Molecule 1 - MUTANT AL2 6E7P9G
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI K-12
    Expression System Plasmid: PAK3000
    Expression System Taxid: 83333
    Expression System Variant: RV308
    Expression System Vector Type: PLASMID
    Fragment: FV FRAGMENT
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: SINGLE CHAIN FV ANTIBODY IN WHICH THE VL AND VH FRAGMENTS ARE JOINED BY A GGGGSGGGGSGGGGSGGGGS LINKER

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1AIC1Ligand/Ion(2S,5R,6R)-6-{[(2R)-2-AMINO-2-PHENYLETHANOYL]AMINO}-3,3-DIMETHYL-7-OXO-4-THIA-1-AZABICYCLO[3.2.0]HEPTANE-2-CARBOXYLIC ACID
2SO42Ligand/IonSULFATE ION
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1AIC1Ligand/Ion(2S,5R,6R)-6-{[(2R)-2-AMINO-2-PHENYLETHANOYL]AMINO}-3,3-DIMETHYL-7-OXO-4-THIA-1-AZABICYCLO[3.2.0]HEPTANE-2-CARBOXYLIC ACID
2SO42Ligand/IonSULFATE ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1AIC-1Ligand/Ion(2S,5R,6R)-6-{[(2R)-2-AMINO-2-PHENYLETHANOYL]AMINO}-3,3-DIMETHYL-7-OXO-4-THIA-1-AZABICYCLO[3.2.0]HEPTANE-2-CARBOXYLIC ACID
2SO4-1Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:11 , LYS A:12 , PHE A:13 , ARG B:111BINDING SITE FOR RESIDUE SO4 A1001
2AC2SOFTWARELYS A:12 , ALA A:103 , HOH A:2106 , HOH A:2159 , ARG B:111BINDING SITE FOR RESIDUE SO4 A1002
3AC3SOFTWAREGLN A:92 , TYR A:97 , LEU A:99 , TRP A:164 , ASN A:166 , ASN A:181 , ALA A:228 , ARG A:229 , TRP A:230 , TRP A:233 , HOH A:2101 , HOH A:2157 , HOH A:2158BINDING SITE FOR RESIDUE AIC A1000

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:26 -A:91
2A:153 -A:227
3B:26 -B:91
4B:153 -B:227

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Tyr A:97 -Pro A:98
2Glu A:137 -Pro A:138
3Tyr B:97 -Pro B:98
4Glu B:137 -Pro B:138

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1H8S)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1H8S)

(-) Exons   (0, 0)

(no "Exon" information available for 1H8S)

(-) 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:220
                                                                                                                                                                                                                                                            
               SCOP domains d1h8sa1 A:4-111 Immunoglobulin light chain kappa variable domain, VL-kappa                                  d1h8sa2 A:132-243 Immunoglobulin heavy chain variable domain, VH                                                 SCOP domains
               CATH domains 1h8sA01 A:4-132 Immunoglobulins                                                                              1h8sA02 A:133-231 Immunoglobulins                                                                  ------------ CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee...eee......eeeeeee.......eeeeee......eeeee...ee.......eeee....eeeeee...hhhhh.eeeeee......ee...eeee...........eeee.....eeeeee....hhhhh.eeeeee......eeeeeee....eeee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeee..ee...eeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1h8s A   4 DIVLTQSHKFMSTSVGDRVSITCKASQDVGTAVAWYQQKPGQSPKLLIYWASTRHTGVPDRFTGSGSGTDFTLTISNVQSEDLADYFCQQYSSYPLTFGAGTKLELKRQVQLQEPGGELVRPGASVKLSCKASGYTFTSYWINWVKQRPGQGLEWIGNIYPSDSYTNYNQKFKDKATLTVDKSSSTAYMQLSSLTSEDSAVYFCARWGYWGQGTLVTVSA 243
                                    13        23        33        43        53        63        73        83        93       103       133       143       153       163       173       183       193       203       213       223       233       243
                                                                                                                                     111|                                                                                                               
                                                                                                                                      132                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:220
                                                                                                                                                                                                                                                            
               SCOP domains d1h8sb1 B:4-112 Immunoglobulin light chain kappa variable domain, VL-kappa                                   d1h8sb2 B:133-243 Immunoglobulin heavy chain variable domain, VH                                                SCOP domains
               CATH domains 1h8sB01 B:4-111 Immunoglobulins                                                                             -1h8sB02 B:133-231 Immunoglobulins                                                                  ------------ CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeee...eeeeee...hhhhh.eeeeee......ee...eeeee..........eeee.....eeeeee....hhhhh.eeeeee......eeeeee......eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeee..ee...eeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1h8s B   4 DIVLTQSHKFMSTSVGDRVSITCKASQDVGTAVAWYQQKPGQSPKLLIYWASTRHTGVPDRFTGSGSGTDFTLTISNVQSEDLADYFCQQYSSYPLTFGAGTKLELKRGVQLQEPGGELVRPGASVKLSCKASGYTFTSYWINWVKQRPGQGLEWIGNIYPSDSYTNYNQKFKDKATLTVDKSSSTAYMQLSSLTSEDSAVYFCARWGYWGQGTLVTVSA 243
                                    13        23        33        43        53        63        73        83        93       103       133       143       153       163       173       183       193       203       213       223       233       243
                                                                                                                                      112|                                                                                                              
                                                                                                                                       133
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 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 1H8S)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1H8S)

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  1h8s
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 Related Entries

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(-) Related Entries Specified in the PDB File

1h8n THREE-DIMENSIONAL STRUCTURE OF ANTI-AMPICILLIN SINGLE CHAIN FV FRAGMENT FROM PHAGE-DISPLAYED MURINE ANTIBODY LIBRARIES
1h8o THREE-DIMENSIONAL STRUCTURE OF ANTI-AMPICILLIN SINGLE CHAIN FV FRAGMENT.