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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PTPN4 PDZ DOMAIN COMPLEXED WITH THE TAILORED PEPTIDE CYTO8-RETEV
 
Authors :  P. Maisonneuve, M. C. Vaney, B. Babault, C. Caillet-Saguy, M. Lafon, M. Delepierre, F. Cordier, N. Wolff
Date :  26 Nov 15  (Deposition) - 08 Jun 16  (Release) - 19 Oct 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.09
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,E  (1x)
Biol. Unit 2:  B,F  (1x)
Biol. Unit 3:  C,G  (1x)
Biol. Unit 4:  D,H  (1x)
Keywords :  Apoptosis, Cell Death, Glioblastoma, Multiprotein Complexes, Pdz Domains, Peptides Design, Protein Binding, Non-Receptor Type 4, Ptpn4, Rabies Virus, Pdz Binding Motif (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Maisonneuve, C. Caillet-Saguy, M. C. Vaney, E. Bibi-Zainab, K. Sawyer, B. Raynal, A. Haouz, M. Delepierre, M. Lafon, F. Cordier, N. Wolff
Molecular Basis Of The Interaction Of The Human Protein Tyrosine Phosphatase Non-Receptor Type 4 (Ptpn4) With The Mitogen-Activated Protein Kinase P38 Gamma.
J. Biol. Chem. V. 291 16699 2016
PubMed-ID: 27246854  |  Reference-DOI: 10.1074/JBC.M115.707208
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 4
    Chains: A, B, C, D
    EC Number: 3.1.3.48
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PDEST15
    Expression System Taxid: 469008
    Expression System Variant: STAR
    Expression System Vector Type: PLASMID
    Fragment: PDZ DOMAIN, RESIDUES 499-604
    Gene: PTPN4
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PROTEIN-TYROSINE PHOSPHATASE MEG1,PTPASE-MEG1
 
Molecule 2 - CYTO8-RETEV
    Chains: E, F, G, H
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): A   E   
Biological Unit 2 (1x):  B   F  
Biological Unit 3 (1x):   C   G 
Biological Unit 4 (1x):    D   H

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:554 , ASN B:514 , ASN C:514 , HOH C:832binding site for residue CL C 701

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:590 -B:590
2C:590 -D:590

(-) Cis Peptide Bonds  (7, 7)

Asymmetric Unit
No.Residues
1Val A:557 -Pro A:558
2His A:593 -Ser A:594
3Val B:557 -Pro B:558
4His B:593 -Ser B:594
5Val C:557 -Pro C:558
6Ser C:594 -Gly C:595
7Val D:557 -Pro D:558

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5EYZ)

(-) 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:93
                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee.........eeeeee....eeeeeeee...hhhhhh........eeeee..ee....hhhhhhhhhhhhhhh....eeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 5eyz A 512 HDNLVLIRMKPDENGRFGFNVKGGYDQKMPVIVSRVAPGTPADLCVPRLNEGDQVVLINGRDIAEHTHDQVVLFIKASCERHSGELMLLVRPN 604
                                   521       531       541       551       561       571       581       591       601   


Chain B from PDB  Type:PROTEIN  Length:94
                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee.........eeeeee....eeeeeeee...hhhhhh........eeeee..ee....hhhhhhhhhhh........eeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                 5eyz B 511 PHDNLVLIRMKPDENGRFGFNVKGGYDQKMPVIVSRVAPGTPADLCVPRLNEGDQVVLINGRDIAEHTHDQVVLFIKASCERHSGELMLLVRPN 604
                                   520       530       540       550       560       570       580       590       600    


Chain C from PDB  Type:PROTEIN  Length:93
                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee.........eeeeee....eeeeeeee...hhhhhh........eeeee..ee....hhhhhhhhhhhhhhh....eeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 5eyz C 512 HDNLVLIRMKPDENGRFGFNVKGGYDQKMPVIVSRVAPGTPADLCVPRLNEGDQVVLINGRDIAEHTHDQVVLFIKASCERHSGELMLLVRPN 604
                                   521       531       541       551       561       571       581       591       601   


Chain D from PDB  Type:PROTEIN  Length:92
                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.........eeeeee....eeeeeeee...hhhhhh........eeeee..ee....hhhhhhhhhhh........eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                 5eyz D 513 DNLVLIRMKPDENGRFGFNVKGGYDQKMPVIVSRVAPGTPADLCVPRLNEGDQVVLINGRDIAEHTHDQVVLFIKASCERHSGELMLLVRPN 604
                                   522       532       542       552       562       572       582       592       602  


Chain E from PDB  Type:PROTEIN  Length:6
                                      
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ..eee. Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 5eyz E   8 GRETEV  13


Chain F from PDB  Type:PROTEIN  Length:6
                                      
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ..eeee Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 5eyz F   8 GRETEV  13


Chain G from PDB  Type:PROTEIN  Length:6
                                      
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ..eee. Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 5eyz G   8 GRETEV  13


Chain H from PDB  Type:PROTEIN  Length:6
                                      
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ..eee. Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 5eyz H   8 GRETEV  13
   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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)

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  5eyz
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  PTN4_HUMAN | P29074
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 Related Entries

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

UniProtKB/Swiss-Prot
        PTN4_HUMAN | P29074: 2cs5 2i75 2vph 3nfk 3nfl 5ez0

(-) Related Entries Specified in the PDB File

3nfk 3NFK CONTAINS THE SAME PDZ DOMAIN OF THE PROTEIN TYROSINE PHOSPHATASE NON RECEPTOR TYPE 4 (PTPN4)
3nfl 3NFL CONTAINS THE SAME PDZ DOMAIN OF THE PROTEIN TYROSINE PHOSPHATASE NON RECEPTOR TYPE 4 (PTPN4)