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(-) Description

Title :  PI3K P85 N-TERMINAL SH2 DOMAIN/CD28-DERIVED PEPTIDE COMPLEX
 
Authors :  S. Inaba, N. Numoto, H. Morii, S. Ogawa, T. Ikura, R. Abe, N. Ito, M. Oda
Date :  30 Jun 16  (Deposition) - 14 Dec 16  (Release) - 10 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  0.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Antigens, Phosphopeptides, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Inaba, N. Numoto, S. Ogawa, H. Morii, T. Ikura, R. Abe, N. Ito, M. Oda
Crystal Structures And Thermodynamic Analysis Reveal Distinct Mechanisms Of Cd28 Phosphopeptide Binding To The Src Homology 2 (Sh2) Domains Of Three Adaptor Proteins
J. Biol. Chem. V. 292 1052 2017
PubMed-ID: 27927989  |  Reference-DOI: 10.1074/JBC.M116.755173

(-) Compounds

Molecule 1 - PHOSPHATIDYLINOSITOL 3-KINASE REGULATORY SUBUNIT ALPHA
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PGEX-4T-2
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Fragment: UNP RESIDUES 325-430
    Gene: PIK3R1, GRB1
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PTDINS-3-KINASE REGULATORY SUBUNIT ALPHA, PHOSPHATIDYLINOSITOL 3-KINASE 85 KDA REGULATORY SUBUNIT ALPHA,PTDINS- 3-KINASE REGULATORY SUBUNIT P85-ALPHA
 
Molecule 2 - T-CELL-SPECIFIC SURFACE GLYCOPROTEIN CD28
    Chains: B
    Engineered: YES
    Fragment: UNP RESIDUES 189-196
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: TP44
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2PTR1Mod. Amino AcidO-PHOSPHOTYROSINE
3SO43Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:377 , LYS A:379 , HIS A:385 , GLY A:388 , HOH A:631 , HOH A:649 , HOH A:676 , HOH A:696 , HOH A:742binding site for residue SO4 A 501
2AC2SOFTWAREARG A:348 , ASP A:349 , ARG A:373 , HOH A:609 , HOH A:613 , HOH A:646 , HOH A:651 , HOH A:670 , HOH A:680binding site for residue SO4 A 502
3AC3SOFTWAREASN A:417 , LYS A:419 , HOH A:602 , HOH A:655 , HOH A:665 , MET B:192 , ASN B:193 , HOH B:306binding site for residue SO4 A 503
4AC4SOFTWARELYS A:382 , TYR A:426 , PRO A:427 , HOH A:629 , MET B:192 , ASN B:193 , MET B:194 , HOH B:303 , HOH B:311 , HOH B:313binding site for residue GOL B 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5GJI)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asp A:394 -Pro A:395

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5GJI)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5GJI)

(-) Exons   (0, 0)

(no "Exon" information available for 5GJI)

(-) 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:107
                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh.......hhhhhhhhhh.....eeeeee........eeeeeee..eeeeeeeeee..eee........hhhhhhhhhhh.hhhhhhhhhh....ee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 5gji A 324 SNMSLQNAEWYWGDISREEVNEKLRDTADGTFLVRDASTKMHGDYTLTLRKGGNNKLIKIFHRDGKYGFSDPLTFSSVVELINHYRNESLAQYNPKLDVKLLYPVSK 430
                                   333       343       353       363       373       383       393       403       413       423       


Chain B 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
                 5gji B 189 SDyMNMTP 196
                              |     
                            191-PTR
   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  (0, 0)

(no "SCOP Domain" information available for 5GJI)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5GJI)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5GJI)

(-) Gene Ontology  (108, 119)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Asp A:394 - Pro A:395   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        CD28_HUMAN | P10747: 1yjd 3wa4 5aul 5gjh
        P85A_HUMAN | P27986: 1a0n 1azg 1h9o 1pbw 1pht 1pic 1pks 1pkt 2iug 2iuh 2iui 2rd0 2v1y 3hhm 3hiz 3i5r 3i5s 4a55 4jps 4l1b 4l23 4l2y 4ovu 4ovv 4waf 4ykn 4zop 5aul 5fi4 5itd 5m6u 5sw8 5swg 5swo 5swp 5swr 5swt 5sx8 5sx9 5sxa 5sxb 5sxc 5sxd 5sxe 5sxf 5sxi 5sxj 5sxk 5ubt 5uk8 5ukj 5ul1 5vlr

(-) Related Entries Specified in the PDB File

5gjh