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(-) Description

Title :  CRYSTAL STRUCTURE OF ANTI-23F STREP FAB C05 WITH RHAMNOSE
 
Authors :  S. Bryson, L. Risnes, S. Damgupta, C. A. Thomson, K. Smith, J. W. Schrade
Date :  11 Mar 14  (Deposition) - 04 Mar 15  (Release) - 04 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.51
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Antibody, Fab Fragment, 23F, Rhamnose, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Bryson, L. Risnes, S. Damgupta, C. A. Thomson, K. Smith, J. W. Schrader, E. F. Pai
Immunoglobulin V-Genes Evolved To Encode Amino Acids That Can Contact Chemically Distinct Antigens To Facilitate The Generation Of Protective Antibodies.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ANTIBODY PN132P2C05, LIGHT CHAIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-DUET
    Expression System Strain: SHUFFLE
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - ANTIBODY PN132P2C05, HEAVY CHAIN
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-DUET
    Expression System Strain: SHUFFLE
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2RAM1Ligand/IonALPHA-L-RHAMNOSE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:32 , LEU A:33 , ALA A:34 , ASP A:50 , GLN A:89 , SER B:100D , PHE B:100F , ALA B:100GBINDING SITE FOR RESIDUE ACT A 501
2AC2SOFTWAREHIS A:38 , VAL A:85 , TYR A:87 , GLN B:39BINDING SITE FOR RESIDUE ACT A 502
3AC3SOFTWAREARG A:91 , SER A:93 , PRO A:95A , GLU B:95 , SER B:187 , LEU B:189 , GLY B:190 , THR B:191 , HOH B:443 , HOH B:504BINDING SITE FOR RESIDUE RAM B 301

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1A:23 -A:88
2A:134 -A:194
3B:22 -B:92
4B:99 -B:100C
5B:140 -B:196

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Ser A:7 -Pro A:8
2Trp A:94 -Pro A:95
3Tyr A:140 -Pro A:141
4Phe B:146 -Pro B:147
5Glu B:148 -Pro B:149

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4PTU)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4PTU)

(-) Exons   (0, 0)

(no "Exon" information available for 4PTU)

(-) 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 A from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                     
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4ptu A    2 IVLTQSPATLSLSPGERGTLSCRASQSVGTYLAWYQHKPGQAPRPLIYDASRRATGIPARFSGSGSGTDFTLTISGLEPEDVAVYYCQHRDSWPPGATFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNR  211
                                    11        21        31        41        51        61        71        81        91    ||  99       109       119       129       139       149       159       169       179       189       199       209  
                                                                                                                        95A|                                                                                                                    
                                                                                                                         95B                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                           
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeeee............eeee...eeeee........eeeee....eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhhhh...eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4ptu B    2 AQLVESGGGVVQPGRSLTLSCAASGFTFSSHGMHWVRQAPGKGLEWVAVIASHGNVNYYADSVKGRFTISRDNSKNTLSLQMDSLRAEDTAVYYCAKESDSCGGDCSRFAFDVWGHGTMVTVSSASTKGPSVFPLAPSGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEP  213
                                    11        21        31        41        51 |      60        70        80  |||   87        97   |||100G|      109       119       135       145       155       165       175       185       195       205        
                                                                             52A                            82A||               100A|||||||                        127|                                                                               
                                                                                                             82B|                100B||||||                         134                                                                               
                                                                                                              82C                 100C|||||                                                                                                           
                                                                                                                                   100D||||                                                                                                           
                                                                                                                                    100E|||                                                                                                           
                                                                                                                                     100F||                                                                                                           
                                                                                                                                      100G|                                                                                                           
                                                                                                                                       100H
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4PTU)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4PTU)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4PTU)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
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  Cis Peptide Bonds
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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

4hh9 SAME V-GENES USED
4hha SAME V-GENES USED
4hie ALTERNATE ANTI-23F ANTIBODY USING SAME V-GENES
4hih ALTERNATE ANTI-23F ANTIBODY USING SAME V-GENES
4hii ALTERNATE ANTI-23F ANTIBODY USING SAME V-GENES
4hij ALTERNATE ANTI-23F ANTIBODY USING SAME V-GENES
4ptt