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(-) Description

Title :  STRUCTURAL BASIS OF PTPN18 FINGERPRINT ON DISTINCT HER2 TYROSINE PHOSPHORYLATION SITES
 
Authors :  H. Wang, F. Yang, D. Yang, Y. Du
Date :  17 Nov 13  (Deposition) - 19 Nov 14  (Release) - 19 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,F  (1x)
Biol. Unit 2:  B,C  (1x)
Biol. Unit 3:  D,E  (1x)
Biol. Unit 4:  G,H  (1x)
Keywords :  Beta Barrel, Beta-Propeller, Kinase Binding, Phosphorylation, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Wang, F. Yang, D. Yang, Y. Du
Structural Basis Of Ptpn18 Fingerprint On Distinct Her2 Tyrosine Phosphorylation Sites
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 18
    Chains: A, B, D, G
    EC Number: 3.1.3.48
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: TYROSINE-PROTEIN PHOSPHATASE DOMAIN (UNP RESIDUES 6-295)
    Gene: PTPN18, BDP1
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: BRAIN-DERIVED PHOSPHATASE
 
Molecule 2 - RECEPTOR TYROSINE-PROTEIN KINASE ERBB-2
    Chains: F, C, E, H
    Engineered: YES
    Fragment: PHOSPHORYLATED PEPTIDE (UNP RESIDUES 1109-1114)
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: METASTATIC LYMPH NODE GENE 19 PROTEIN, MLN 19, PROTO- ONCOGENE NEU, PROTO-ONCOGENE C-ERBB-2, TYROSINE KINASE-TYPE CELL SURFACE RECEPTOR HER2, P185ERBB2
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): A    F  
Biological Unit 2 (1x):  BC     
Biological Unit 3 (1x):    DE   
Biological Unit 4 (1x):       GH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1PTR4Mod. Amino AcidO-PHOSPHOTYROSINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1PTR1Mod. Amino AcidO-PHOSPHOTYROSINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1PTR1Mod. Amino AcidO-PHOSPHOTYROSINE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1PTR1Mod. Amino AcidO-PHOSPHOTYROSINE
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1PTR1Mod. Amino AcidO-PHOSPHOTYROSINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR B:62 , LYS B:63 , ASP B:64 , ASP B:197 , ARG B:198 , SER B:229 , SER B:230 , ALA B:231 , GLY B:232 , CYS B:233 , GLY B:234 , ARG B:235 , GLN B:276BINDING SITE FOR CHAIN C OF RECEPTOR TYROSINE- PROTEIN KINASE ERBB-2
2AC2SOFTWARETYR D:62 , LYS D:63 , ASP D:64 , ARG D:140 , ASP D:197 , ARG D:198 , SER D:229 , SER D:230 , ALA D:231 , GLY D:232 , CYS D:233 , GLY D:234 , ARG D:235 , GLN D:276 , HOH D:301BINDING SITE FOR CHAIN E OF RECEPTOR TYROSINE- PROTEIN KINASE ERBB-2
3AC3SOFTWARETYR A:62 , LYS A:63 , ASP A:64 , ASP A:197 , ARG A:198 , SER A:229 , SER A:230 , ALA A:231 , GLY A:232 , CYS A:233 , GLY A:234 , ARG A:235 , GLN A:276BINDING SITE FOR CHAIN F OF RECEPTOR TYROSINE- PROTEIN KINASE ERBB-2
4AC4SOFTWARETYR G:62 , LYS G:63 , ASP G:64 , VAL G:65 , ARG G:138 , ASP G:197 , ARG G:198 , SER G:229 , SER G:230 , ALA G:231 , GLY G:232 , CYS G:233 , GLY G:234 , ARG G:235 , GLN G:276 , HOH G:301 , HOH H:201BINDING SITE FOR CHAIN H OF RECEPTOR TYROSINE- PROTEIN KINASE ERBB-2

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4NND)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Val A:25 -Leu A:26
2Val B:25 -Leu B:26
3Val D:25 -Leu D:26
4Val G:25 -Leu G:26

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4NND)

(-) 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:283
                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh....hhhhhh..hhhhh.......hhh.eee...hhhhh...eeeeeeee.....eeeeee...hhhhhhhhhhhhhhh...eeee......................eee..eeeeeeeeeeee..eeeeeeeeee..eeeeeeeeee..........hhhhhhhhhhhhhhhhh.....eeee....hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nnd A   6 DSARSFLERLEARAVLAGEFSDIQACSAAWKADGVCSTVAGSRPENVRKNRYKDVLPYDQTRVILSLLQEEGHSDYINGNFIRGVDGSLAYIATQGPLPHTLLDFWRLVWEFGVKVILMACREIENGRKRCERYWAQEQEPLQTGLFCITLIKEKWLNEDIMLRTLKVTFQKESRSVYQLQYMSWPDRGVPSSPDHMLAMVEEARRLQGSGPEPLCVHSSAGCGRTGVLCTVDYVRQLLLTMIPPDFSLFDVVLKMRKQRPAAVQTEEQYRFLYHTVAQMFCS 294
                                    15  ||    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250||     261       271       281       291   
                                       18|                                                                                                                                                                                                                                251|                                         
                                        24                                                                                                                                                                                                                                 253                                         


Chain B from PDB  Type:PROTEIN  Length:283
                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh....hhhhhh..hhhhh.......hhh.eee...hhhhh...eeeeeeee.....eeeeee...hhhhhhhhhhhhhhh...eeee......................eee..eeeeeeeeeeee..eeeeeeeeee..eeeeeeeeee..........hhhhhhhhhhhhhhhhh.....eeee....hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nnd B   6 DSARSFLERLEARVLAGEFSDIQACSAAWKADGVCSTVAGSRPENVRKNRYKDVLPYDQTRVILSLLQEEGHSDYINGNFIRGVDGSLAYIATQGPLPHTLLDFWRLVWEFGVKVILMACREIENGRKRCERYWAQEQEPLQTGLFCITLIKEKWLNEDIMLRTLKVTFQKESRSVYQLQYMSWPDRGVPSSPDHMLAMVEEARRLQGSGPEPLCVHSSAGCGRTGVLCTVDYVRQLLLTQMIPPDFSLFDVVLKMRKQRPAAVQTEEQYRFLYHTVAQMFCS 294
                                    15  ||    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291   
                                       18|                                                                                                                                                                                                                                                                             
                                        25                                                                                                                                                                                                                                                                             


Chain C from PDB  Type:PROTEIN  Length:6
                                      
               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
                 4nnd C 109 LQRySE 114
                               |  
                             112-PTR


Chain D from PDB  Type:PROTEIN  Length:281
                                                                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh..hhhhhhhhhhhhhhhhhh............hhhhh.......hhh.eee..........eeeeeeee.....eeeeee...hhhhhhhhhhhhhhh...eeee......................eee..eeeeeeeeeeee..eeeeeeeeee..eeeeeeeeee..........hhhhhhhhhhhhhhhhh.....eeee....hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nnd D   6 DSARSFLERLEAVLAGEFSDIQACSAAWKADGVCSTVAGSRPENVRKNRYKDVLPYDQTRVILSLLQEEHSDYINGNFIRGVDGSLAYIATQGPLPHTLLDFWRLVWEFGVKVILMACREIENGRKRCERYWAQEQEPLQTGLFCITLIKEKWLNEDIMLRTLKVTFQKESRSVYQLQYMSWPDRGVPSSPDHMLAMVEEARRLQGSGPEPLCVHSSAGCGRTGVLCTVDYVRQLLLTQMIPPDFSLFDVVLKMRKQRPAAVQTEEQYRFLYHTVAQMFCS 294
                                    15 ||     32        42        52        62        72        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293 
                                      17|                                                      81|                                                                                                                                                                                                                   
                                       25                                                       83                                                                                                                                                                                                                   


Chain E from PDB  Type:PROTEIN  Length:5
                                     
               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
                 4nnd E 109 LQRyS 113
                               | 
                             112-PTR


Chain F from PDB  Type:PROTEIN  Length:6
                                      
               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
                 4nnd F 109 LQRySE 114
                               |  
                               |  
                             112-PTR


Chain G from PDB  Type:PROTEIN  Length:278
                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh..hhhhhhhhhhhhhhhhhh....hhhhhh..hhhhh.......hhh.eee..........eeeeeeee.....eeeeee...hhhhhhhhhhhhhhh...eeee......................eee..eeeeeeeeeeee..eeeeeeeeee..eeeeeeeeee..........hhhhhhhhhhhhhhhh.....eeee....hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nnd G   6 DSARSFLERLVLAGEFSDIQACSAAWKADGVCSTVAGSRPENVRKNRYKDVLPYDQTRVILSLLQEEHSDYINGNFIRGVDGSLAYIATQGPLPHTLLDFWRLVWEFGVKVILMACREIENGRKRCERYWAQEQEPLQTGLFCITLIKEKWLNEDIMLRTLKVTFQKESRSVYQLQYMSWPDRGVPSPDHMLAMVEEARRLQGSGPEPLCVHSSAGCGRTGVLCTVDYVRQLLLTQMIPPDFSLFDVVLKMRKQRPAAVQTEEQYRFLYHTVAQMFCS 294
                                    15|       34        44        54        64        74      ||85        95       105       115       125       135       145       155       165       175       185       195     ||206       216       226       236       246       256       266       276       286        
                                    15|                                                      81|                                                                                                                   201|                                                                                           
                                     25                                                       83                                                                                                                    203                                                                                           


Chain H from PDB  Type:PROTEIN  Length:5
                                     
               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
                 4nnd H 109 LQRyS 113
                               | 
                             112-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  (0, 0)

(no "SCOP Domain" information available for 4NND)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (81, 84)

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  4nnd
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  ERBB2_HUMAN | P04626
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  PTN18_HUMAN | Q99952
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 Related Entries

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

UniProtKB/Swiss-Prot
        ERBB2_HUMAN | P04626: 1mfg 1mfl 1mw4 1n8z 1ovc 1qr1 1s78 2a91 2jwa 2ks1 2l4k 2n2a 3be1 3h3b 3mzw 3n85 3pp0 3rcd 3wlw 3wsq 4gfu 4hrl 4hrm 4hrn 5k33 5kwg
        PTN18_HUMAN | Q99952: 2oc3 4gfu 4gfv

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4NND)