Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
(-)Biological Unit 3
(-)Biological Unit 4
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)
Image Biological Unit 4
Biological Unit 4  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE PTPN4 PDZ DOMAIN COMPLEXED WITH THE PDZ BINDING MOTIF OF THE MITOGEN ACTIVATED PROTEIN KINASE P38GAMMA.
 
Authors :  P. Maisonneuve, M. C. Vaney, C. Caillet-Saguy, M. Lafon, M. Delepierre F. Cordier, N. Wolff
Date :  26 Nov 15  (Deposition) - 08 Jun 16  (Release) - 17 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
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, P38Gamma, Mitogen Activated Protein Kinase, 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 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 - MITOGEN-ACTIVATED PROTEIN KINASE 12
    Chains: E, F, G, H
    Engineered: YES
    Fragment: PDZ BINDING MOTIF, RESIDUES 269-277
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: MITOGEN-ACTIVATED PROTEIN KINASE 12,ISOFORM CRA_A
    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, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1SO4-1Ligand/IonSULFATE ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1SO4-1Ligand/IonSULFATE ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS D:533 , MET D:540 , VAL H:7 , SER H:8binding site for residue SO4 D 701
2AC2SOFTWARELYS C:533 , LYS C:539 , MET C:540 , VAL G:7 , SER G:8binding site for residue SO4 G 101

(-) SS Bonds  (2, 2)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Val A:557 -Pro A:558
2Val B:557 -Pro B:558
3Val C:557 -Pro C:558
4Val D:557 -Pro D:558

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5EZ0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5EZ0)

(-) Exons   (0, 0)

(no "Exon" information available for 5EZ0)

(-) 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:90
                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeee.........eeeeee....eeeeeeee...hhhhhh........eeeee..ee....hhhhhhhhhh.....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------ Transcript
                 5ez0 A 511 PHDNLVLIRMKPDENGRFGFNVKGGYDQKMPVIVSRVAPGTPADLCVPRLNEGDQVVLINGRDIAEHTHDQVVLFIKASCGELMLLVRPN 604
                                   520       530       540       550       560       570       580       590|      604
                                                                                                         590|         
                                                                                                          595         


Chain B from PDB  Type:PROTEIN  Length:92
                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee.........eeee.........eeeee...hhhhhh........eeeee..ee....hhhhhhhhhh......eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                 5ez0 B 510 IPHDNLVLIRMKPDENGRFGFNVKGGYDQKMPVIVSRVAPGTPADLCVPRLNEGDQVVLINGRDIAEHTHDQVVLFIKASCSGELMLLVRPN 604
                                   519       529       539       549       559       569       579       589||     602  
                                                                                                          590|          
                                                                                                           594          


Chain C from PDB  Type:PROTEIN  Length:94
                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee.........eeee.........eeeee...hhhhhh........eeeee..ee....hhhhhhhhhhhhhhhhhhheeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                 5ez0 C 511 PHDNLVLIRMKPDENGRFGFNVKGGYDQKMPVIVSRVAPGTPADLCVPRLNEGDQVVLINGRDIAEHTHDQVVLFIKASCERHSGELMLLVRPN 604
                                   520       530       540       550       560       570       580       590       600    


Chain D from PDB  Type:PROTEIN  Length:95
                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee.........eeee.........eeeee...hhhhhh........eeeee..ee....hhhhhhhhhhhhhhhhhhheeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------- Transcript
                 5ez0 D 510 IPHDNLVLIRMKPDENGRFGFNVKGGYDQKMPVIVSRVAPGTPADLCVPRLNEGDQVVLINGRDIAEHTHDQVVLFIKASCERHSGELMLLVRPN 604
                                   519       529       539       549       559       569       579       589       599     


Chain E 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
                 5ez0 E   8 SKETPL  13


Chain F 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
                 5ez0 F   8 SKETPL  13


Chain G from PDB  Type:PROTEIN  Length:11
                                           
               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
                 5ez0 G   3 SWARVSKETPL  13
                                    12 


Chain H from PDB  Type:PROTEIN  Length:11
                                           
               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
                 5ez0 H   3 SWARVSKETPL  13
                                    12
   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 5EZ0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5EZ0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5EZ0)

(-) Gene Ontology  (26, 27)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Val A:557 - Pro A:558   [ RasMol ]  
    Val B:557 - Pro B:558   [ RasMol ]  
    Val C:557 - Pro C:558   [ RasMol ]  
    Val D:557 - Pro D:558   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]
    Biological Unit 4  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format | Biol. Unit 3 PNG format | Biol. Unit 4 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5ez0
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  B5MDL5_HUMAN | B5MDL5
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
  PTN4_HUMAN | P29074
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.1.3.48
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  B5MDL5_HUMAN | B5MDL5
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  PTN4_HUMAN | P29074
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

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

(-) 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)
5eyz 5EYZ CONTAINS THE SAME PDZ DOMAIN OF THE PROTEIN TYROSINE PHOSPHATASE NON RECEPTOR TYPE 4 (PTPN4)