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(-) Description

Title :  CRYSTAL STRUCTURE OF THE SGIP1 MU HOMOLOGY DOMAIN IN COMPLEX WITH AN EPS15 FRAGMENT CONTAINING TWO DPF MOTIFS (YDPFGGDPFKG)
 
Authors :  A. Shimada, A. Yamaguchi, D. Kohda
Date :  08 Jul 15  (Deposition) - 06 Jul 16  (Release) - 06 Jul 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Endocytosis, Protein-Protein Interaction (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Shimada, A. Yamaguchi, D. Kohda
Structural Basis For The Recognition Of Two Consecutive Mutually Interacting Dpf Motifs By The Sgip1 Mu Homology Domain.
Sci Rep V. 6 19565 2016
PubMed-ID: 26822536  |  Reference-DOI: 10.1038/SREP19565

(-) Compounds

Molecule 1 - SH3-CONTAINING GRB2-LIKE PROTEIN 3-INTERACTING PROTEIN 1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-6P-1
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 552-828
    Gene: SGIP1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ENDOPHILIN-3-INTERACTING PROTEIN
 
Molecule 2 - EPIDERMAL GROWTH FACTOR RECEPTOR SUBSTRATE 15
    Chains: B
    Engineered: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: EPS15
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric/Biological Unit (1, 6)
No.NameCountTypeFull Name
1ZN6Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:558 , HIS A:601binding site for residue ZN A 901
2AC2SOFTWAREGLU A:589 , ASP A:672 , HOH A:1032binding site for residue ZN A 902
3AC3SOFTWAREHIS A:655 , HOH A:1031binding site for residue ZN A 903
4AC4SOFTWAREHIS A:623 , ASP A:639 , HOH A:1004binding site for residue ZN A 904
5AC5SOFTWAREHIS A:623 , GLU A:644 , GLN A:677binding site for residue ZN A 905
6AC6SOFTWAREASP A:758binding site for residue ZN A 906

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:633 -A:633

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Leu A:740 -Pro A:741
2Gly A:780 -Pro A:781

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5AWT)

(-) 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:266
                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeeeeeee..hhhhheeeeeeeeeeeee.hhhhhhhhh......eeeee....eeeeee..........eeeee.hhhhhhhhhhhhhhhh....eeeeeeeeeee..hhhhhh.eeeeeeeeee..eeeeeeeeee.hhhh.....eeeeeeeee....eeeeeeee...eee....eeeeeeeee........eeeeeeeeee.........eeeeeeee.......eeeee...eeeeeeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5awt A 558 DTLPVAAAFTETVNAYFKGADPSKCIVKITGEMVLSFPAGITRHFANNPSPAALTFRVINFSRLEHVLPNPQLLCCDANTKEFWVNMPNLMTHLKKVSEQKPQATYYNVDMLKYQVSAQGIQSTPLNLAVNWRCEPSSTDLRIDYKYNTDAMTTAVALNNVQFLVPIDGGVTKLQAVLPPAVWNAEQQRILWKIPDISQKSENGGVGSLLARFQLSEGPSKPSPLVVQFTSEGSTLSGCDIELVGAGYRFSLIKKRFAAGKYLADN 828
                                   567       577       587       597       607       617       627     ||642       652       662       672       682       692       702       712       722       732       742       752       762       772       782       792       802       812       822      
                                                                                                     633|                                                                                                                                                                                             
                                                                                                      639                                                                                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:10
                                          
               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
                 5awt B 639 YDPFGGDPFK 648
                                   648
   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 5AWT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (36, 45)

Asymmetric/Biological Unit(hide GO term definitions)

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  5awt
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  EPS15_HUMAN | P42566
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  SGIP1_HUMAN | Q9BQI5
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 Related Entries

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

UniProtKB/Swiss-Prot
        EPS15_HUMAN | P42566: 1c07 1eh2 1f8h 1ff1 2iv9 2jxc 4rh5 4rh9 4rhg 4s0g 5awu 5jp2
        SGIP1_HUMAN | Q9BQI5: 5awr 5aws 5awu

(-) Related Entries Specified in the PDB File

5awr THE SAME PROTEIN
5aws ONE OF TWO IS THE SAME PROTEIN
5awu