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(-) Description

Title :  CRYSTAL STRUCTURE OF THE SYNTENIN PDZ1 AND PDZ2 TANDEM IN COMPLEX WITH THE FRIZZLED 7 C-TERMINAL FRAGMENT AND PIP2
 
Authors :  A. L. Egea-Jimenez, R. Gallardo, A. Garcia-Pino, Y. Ivarsson, A. M. Waw R. Kashyap, R. Loris, J. Schymkowitz, F. Rousseau, P. Zimmermann
Date :  30 Mar 15  (Deposition) - 29 Jun 16  (Release) - 29 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.45
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Syntenin, Pdz, Pip2, Frizzle 7, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. L. Egea-Jimenez, R. Gallardo, A. Garcia-Pino, Y. Ivarsson, A. M. Wawrzyniak, R. Kashyap, R. Loris, J. Schymkowitz, F. Rousseau, P. Zimmermann
Crystal Structure Of The Syntenin Pdz1 And Pdz2 Tandem In Complex With The Frizzled 7 C-Terminal Fragment And Pip2
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - SYNTENIN-1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Taxid: 511693
    Fragment: RESIDUES 111-275
    Gene: SDCBP, MDA9, SYCL
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: MELANOMA DIFFERENTIATION-ASSOCIATED PROTEIN 9,MDA-9,PRO-TGF- ALPHA CYTOPLASMIC DOMAIN-INTERACTING PROTEIN 18,TACIP18,SCAFFOLD PROTEIN PBP1,SYNDECAN-BINDING PROTEIN 1
 
Molecule 2 - LYS-GLY-GLU-THR-ALA-VAL
    Chains: C, D
    Engineered: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric Unit (3, 7)
No.NameCountTypeFull Name
1ACT4Ligand/IonACETATE ION
2GOL2Ligand/IonGLYCEROL
3IP21Ligand/IonD-MYO-INOSITOL-4,5-BISPHOSPHATE
Biological Unit 1 (3, 4)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2GOL2Ligand/IonGLYCEROL
3IP21Ligand/IonD-MYO-INOSITOL-4,5-BISPHOSPHATE
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
2GOL-1Ligand/IonGLYCEROL
3IP2-1Ligand/IonD-MYO-INOSITOL-4,5-BISPHOSPHATE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:173 , ASP A:256 , SER A:259 , HOH A:411 , LYS B:176binding site for residue ACT A 301
2AC2SOFTWAREHIS A:202 , SER A:226 , ARG A:229 , ASN A:230 , HOH A:431binding site for residue GOL A 302
3AC3SOFTWARELYS A:124 , ILE A:125 , GLY A:126 , LEU A:127 , HOH A:447binding site for residue GOL A 303
4AC4SOFTWAREASN A:215 , LYS A:250 , ASP A:251 , LYS C:1binding site for residue IP2 A 304
5AC5SOFTWARELYS B:124 , ILE B:125 , GLY B:126 , LEU B:127binding site for residue ACT B 301
6AC6SOFTWAREASN B:144 , SER B:145 , HIS B:202 , SER B:226 , ARG B:229 , ASN B:230 , HOH B:446binding site for residue ACT B 302
7AC7SOFTWARELEU B:249 , LYS B:250 , GLN B:253binding site for residue ACT B 303

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Z33)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4Z33)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Z33)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Z33)

(-) Exons   (0, 0)

(no "Exon" information available for 4Z33)

(-) 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:166
                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.........eeeeee..eeeeeee...hhhhhh......eeeee..ee....hhhhhhhhhhh.....eeeeee.....eeeeee........eeee..eeeee...hhhhhh.....eeeeee..ee....hhhhhhhhhhh...eeeeeeee.hhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4z33 A 110 SGIREVILCKDQDGKIGLRLKSIDNGIFVQLVQANSPASLVGLRFGDQVLQINGENCAGWSSDKAHKVLKQAFGEKITMTIRDRPFERTITMHKDSTGHVGFIFKNGKITSIVKDSSAARNGLLTEHNICEINGQNVIGLKDSQIADILSTSGTVVTITIMPAFIF 275
                                   119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269      


Chain B from PDB  Type:PROTEIN  Length:165
                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.........eeeeee..eeeeeee...hhhhhh......eeeee..ee....hhhhhhhhhhhh....eeeeee.....eeeeee........eeee..eeeee...hhhhhh.....eeeeee..ee....hhhhhhhhhhhh..eeeeeeee.hhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4z33 B 111 GIREVILCKDQDGKIGLRLKSIDNGIFVQLVQANSPASLVGLRFGDQVLQINGENCAGWSSDKAHKVLKQAFGEKITMTIRDRPFERTITMHKDSTGHVGFIFKNGKITSIVKDSSAARNGLLTEHNICEINGQNVIGLKDSQIADILSTSGTVVTITIMPAFIF 275
                                   120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270     


Chain C 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
                 4z33 C   1 KGETAV   6


Chain D from PDB  Type:PROTEIN  Length:4
                                    
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .ee. Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                 4z33 D   3 ETAV   6
   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 4Z33)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Z33)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Z33)

(-) Gene Ontology  (83, 89)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        FZD7_HUMAN | O75084: 5t44 5urv
        SDCB1_HUMAN | O00560: 1n99 1nte 1obx 1oby 1obz 1r6j 1v1t 1w9e 1w9o 1w9q 1ybo

(-) Related Entries Specified in the PDB File

1n99 1N99 CONTAINS THE SAME PROTEIN