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(-) Description

Title :  STRUCTURE OF PHOSPHOSERINE/THREONINE (PSTAB) SCAFFOLD BOUND TO PTHR PEPTIDE
 
Authors :  J. T. Koerber, N. D. Thomsen, B. T. Hannigan, W. F. Degrado, J. A. Wells
Date :  28 Feb 13  (Deposition) - 28 Aug 13  (Release) - 26 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym./Biol. Unit :  H,L,P
Keywords :  Immmunoglobulin Domain, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. T. Koerber, N. D. Thomsen, B. T. Hannigan, W. F. Degrado, J. A. Wells
Nature-Inspired Design Of Motif-Specific Antibody Scaffolds
Nat. Biotechnol. V. 31 916 2013
PubMed-ID: 23955275  |  Reference-DOI: 10.1038/NBT.2672

(-) Compounds

Molecule 1 - FAB LIGHT CHAIN
    ChainsL
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainC43 PRO+
    Expression System Taxid562
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
 
Molecule 2 - FAB HEAVY CHAIN
    ChainsH
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainC43 PRO+
    Expression System Taxid562
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
 
Molecule 3 - PHOSPHOPEPTIDE
    ChainsP
    EngineeredYES
    SyntheticYES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit HLP

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1PPI1Ligand/IonPROPANOIC ACID
2TPO1Mod. Amino AcidPHOSPHOTHREONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO H:123 , SER L:121 , ASP L:122 , SER L:123 , HOH L:479 , HOH L:616BINDING SITE FOR RESIDUE PPI L 301
2AC2SOFTWARESER H:52 , THR H:52A , PRO H:52B , ARG H:53 , GLY H:54 , SER H:55 , THR H:56 , TYR H:58 , SER H:98 , THR H:99 , SER H:100 , TYR H:100A , HOH H:559 , HOH H:570 , SER L:91 , PHE L:92 , ASN L:93 , VAL L:94 , ALA L:184 , GLU L:187 , LYS L:188 , HIS L:189 , LYS L:190 , ARG L:211 , HOH L:526 , HOH L:539 , HOH P:101 , HOH P:102 , HOH P:103 , HOH P:105 , HOH P:106 , HOH P:107 , HOH P:108 , HOH P:109 , HOH P:110 , HOH P:113BINDING SITE FOR CHAIN P OF PHOSPHOPEPTIDE

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:92
2H:140 -H:196
3L:23 -L:88
4L:134 -L:194
5L:214 -H:216

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Ser L:7 -Pro L:8
2Val L:94 -Pro L:95
3Tyr L:140 -Pro L:141
4Thr H:52A-Pro H:52B
5Phe H:146 -Pro H:147
6Glu H:148 -Pro H:149

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4JG1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4JG1)

(-) Exons   (0, 0)

(no "Exon" information available for 4JG1)

(-) 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:225
                                                                                                                                                                                                                                                                  
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee.......eee.......eeeeeehhh.eeeeee...hhhhheeeeeeeeee..eeeeeee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4jg1 H    0 SEVQLVESGGGLVQPGGSLRLSCVTSGFTFRKFGMSWVRQAPGKGLEWVASISTPRGSTTYYSDSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCTRGYSSTSYAMDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC  216
                                     9        19        29        39        49   ||   57        67        77     |||84        94      |101       111       121       131       141       151       161       171       181       191       201       211     
                                                                               52A|                            82A||               100A||                                                                                                                    
                                                                                52B                             82B|                100B|                                                                                                                    
                                                                                                                 82C                 100C                                                                                                                    

Chain L from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                       
               SCOP domains d4jg1l1 L:1-107 automated matches                                                                          d4jg1l2 L:108-214 automated matches                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4jg1 L    1 DIVLTQSPATLSLSPGERATLSCMTSTDIDDDMNWYQQKPGQAPRLLISEGNTLRPGVPARFSGSGSGTDFTLTISSLEPEDFAVYYCLQSFNVPLTFGQGTKVEIKRTVAAPSVFIFPPSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC  214
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210    

Chain P from PDB  Type:PROTEIN  Length:9
                                          
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ......... Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                4jg1 P    1 KGNYVVTtH    9
                                   | 
                                   8-TPO

   Legend:   → Mismatch (orange background)
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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  (2, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4JG1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4JG1)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4JG1)

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  Cis Peptide Bonds
    Glu H:148 - Pro H:149   [ RasMol ]  
    Phe H:146 - Pro H:147   [ RasMol ]  
    Ser L:7 - Pro L:8   [ RasMol ]  
    Thr H:52A - Pro H:52B  [ RasMol ]  
    Tyr L:140 - Pro L:141   [ RasMol ]  
    Val L:94 - Pro L:95   [ RasMol ]  
 

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 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 4JG1)

(-) Related Entries Specified in the PDB File

4jfx 4jfy 4jfz 4jg1