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(-) Description

Title :  STRUCTURE OF PHOSPHOTYROSINE (PTYR) SCAFFOLD BOUND TO PTYR PEPTIDE
 
Authors :  J. T. Koerber, N. D. Thomsen, B. T. Hannigan, W. F. Degrado, J. A. Wells
Date :  28 Feb 13  (Deposition) - 25 Sep 13  (Release) - 26 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B,H,L,P
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  H,L,P  (1x)
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
    Chains: A, L
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: C43 PRO+
    Expression System Taxid: 562
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - FAB HEAVY CHAIN
    Chains: B, H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: C43 PRO+
    Expression System Taxid: 562
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - PHOSPHOPEPTIDE
    Chains: P
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit : ABHLP
Biological Unit 1 (1x): AB   
Biological Unit 2 (1x):   HLP

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1PG42Ligand/IonTETRAETHYLENE GLYCOL
2PTR1Mod. Amino AcidO-PHOSPHOTYROSINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1PG41Ligand/IonTETRAETHYLENE GLYCOL
2PTR-1Mod. Amino AcidO-PHOSPHOTYROSINE
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1PG41Ligand/IonTETRAETHYLENE GLYCOL
2PTR1Mod. Amino AcidO-PHOSPHOTYROSINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:9 , TYR A:87 , GLN A:100 , GLY A:101 , HOH A:577 , HOH A:625 , HOH A:647 , HOH A:649 , GLY B:42 , LYS B:43BINDING SITE FOR RESIDUE PG4 A 301
2AC2SOFTWAREGLY H:42 , LYS H:43 , ALA L:9 , TYR L:87 , GLN L:100 , GLY L:101 , HOH L:474 , HOH L:561 , HOH L:616BINDING SITE FOR RESIDUE PG4 L 301
3AC3SOFTWAREVAL H:52 , THR H:52A , GLY H:53 , ARG H:55 , LYS H:56 , TYR H:58 , SER H:98 , THR H:99 , SER H:100 , TYR H:100A , HOH H:436 , SER L:91 , PHE L:92 , ASN L:93 , VAL L:94 , HOH P:101 , HOH P:102 , HOH P:103 , HOH P:104BINDING SITE FOR CHAIN P OF PHOSPHOPEPTIDE

(-) SS Bonds  (9, 9)

Asymmetric Unit
No.Residues
1A:23 -A:88
2A:134 -A:194
3A:214 -B:216
4B:22 -B:92
5B:140 -B:196
6H:22 -H:92
7H:140 -H:196
8L:23 -L:88
9L:134 -L:194

(-) Cis Peptide Bonds  (10, 10)

Asymmetric Unit
No.Residues
1Ser A:7 -Pro A:8
2Val A:94 -Pro A:95
3Tyr A:140 -Pro A:141
4Phe B:146 -Pro B:147
5Glu B:148 -Pro B:149
6Ser L:7 -Pro L:8
7Val L:94 -Pro L:95
8Tyr L:140 -Pro L:141
9Phe H:146 -Pro H:147
10Glu H:148 -Pro H:149

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4JFX)

(-) 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:214
                                                                                                                                                                                                                                                       
               SCOP domains d4jfxa1 A:1-107 automated matches                                                                          d4jfxa2 A: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..hhhhhhh.eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4jfx A    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 B 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.......eeeeee....eeeeee...hhhhheeeeeeeeee..eeeeeee...eeeee........eeeee......eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4jfx B   -2 EISEVQLVESGGGLVQPGGSLRLSCVTSGFTFRKFGMSWVRQAPGKGLEWVASIVTGGRKTYYSDSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCTRGYSSTSYAMDYWGQGTLVTVSSASTKGPSVFPLAPSSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKS  219
                                     7        17        27        37        47     |  56        66        76      ||83        93      100C       110       120      |134       144       154       164       174       184       194       204       214     
                                                                                 52A                            82A||               100A||                        127|                                                                                       
                                                                                                                 82B|                100B|                         132                                                                                       
                                                                                                                  82C                 100C                                                                                                                   


Chain H from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                            
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeeeeee..eeeeeee...eeeee........eeeee.......eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4jfx H    1 EVQLVESGGGLVQPGGSLRLSCVTSGFTFRKFGMSWVRQAPGKGLEWVASIVTGGRKTYYSDSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCTRGYSSTSYAMDYWGQGTLVTVSSASTKGPSVFPLAPSSKGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKS  215
                                    10        20        30        40        50  |     59        69        79   |||  86        96    |||103       113       123     ||136       146       156       166       176       186       196       206         
                                                                              52A                            82A||               100A||                          129|                                                                                  
                                                                                                              82B|                100B|                           133                                                                                  
                                                                                                               82C                 100C                                                                                                                


Chain L from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                       
               SCOP domains d4jfxl1 L:1-107 automated matches                                                                          d4jfxl2 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..hhhhhhh.eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4jfx 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:8
                                         
               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
                4jfx P    2 GNYVVTyA    9
                                  | 
                                  8-PTR
   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, 4)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

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  4jfx
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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

4jfy 4jfz 4jg0 4jg1