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(-) Description

Title :  STRUCTURE OF THE STAPLED PEPTIDE BOUND TO MDM2
 
Authors :  Y. H. Lau, Y. Wu, M. Rossmann, P. De Andrade, Y. S. Tan, G. J. Mckenzie, A. R. Venkitaraman, M. Hyvonen, D. R. Spring
Date :  22 Jan 15  (Deposition) - 27 Jan 16  (Release) - 27 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ligase, Mdm2 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. H. Lau, Y. Wu, M. Rossmann, B. X. Tan, P. De Andrade, Y. S. Tan, C. Verma, G. J. Mckenzie, A. R. Venkitaraman, M. Hyvonen, D. R. Spring
Double Strain-Promoted Macrocyclization For The Rapid Selection Of Cell-Active Stapled Peptides.
Angew. Chem. Int. Ed. Engl. V. 54 15410 2015
PubMed-ID: 26768531  |  Reference-DOI: 10.1002/ANIE.201508416

(-) Compounds

Molecule 1 - E3 UBIQUITIN-PROTEIN LIGASE MDM2
    Chains: A
    EC Number: 6.3.2.19
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX6P1
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: P53 BINDING DOMAIN (RESIDUES 17-108)
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - STAPLED PEPTIDE
    Chains: B
    Organism Scientific: SYHTHETIC CONSTRUCT
    Organism Taxid: 32630
    Other Details: SYNTHETIC PEPTIDE WITH A NIS-TRAZOLYL STAPLE BETWEEN AMINO ACIDS 4 AND 11
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1LAY1Mod. Amino AcidN-ACETYL-L-LEUCINE
2P071Ligand/Ion1,8-DIETHYL-1,8-DIHYDRODIBENZO[3,4:7,8][1,2,3]TRIAZOLO[4',5':5,6]CYCLOOCTA[1,2-D][1,2,3]TRIAZOLE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:55 , MET A:62 , ARG A:97 , TYR A:100 , THR A:101 , TYR A:104 , ALA B:4 , TRP B:7 , ALA B:8 , ALA B:11 , HOH B:2012BINDING SITE FOR RESIDUE P07 B1030

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5AFG)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5AFG)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5AFG)

(-) 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:83
                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee..hhhhhhhhhh.......eehhhhhhhhhhhhhhh.........eee...hhhhhhhh..eee..hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------- Transcript
                 5afg A  26 TLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDAAQQHIVYCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLV 108
                                    35        45        55        65        75        85        95       105   


Chain B from PDB  Type:PROTEIN  Length:12
                                            
               SCOP domains ------------ SCOP domains
               CATH domains ------------ CATH domains
               Pfam domains ------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------ SAPs(SNPs)
                    PROSITE ------------ PROSITE
                 Transcript ------------ Transcript
                 5afg B   1 xTFAEYWAQLAS  12
                            |       10  
                            1-LAY
   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 5AFG)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (83, 83)

Asymmetric/Biological Unit(hide GO term definitions)

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  5afg
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 Related Entries

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

UniProtKB/Swiss-Prot
        MDM2_HUMAN | Q00987: 1rv1 1t4e 1t4f 1ycr 1z1m 2axi 2c6a 2c6b 2f1y 2fop 2gv2 2hdp 2lzg 2m86 2mps 2ruh 2vje 2vjf 3eqs 3g03 3iux 3iwy 3jzk 3jzr 3jzs 3lbk 3lbl 3lnj 3lnz 3mqs 3tj2 3tpx 3tu1 3v3b 3vbg 3vzv 3w69 4dij 4ere 4erf 4hbm 4hfz 4hg7 4jv7 4jv9 4jve 4jvr 4jwr 4mdn 4mdq 4oas 4oba 4occ 4ode 4odf 4ogn 4ogt 4ogv 4oq3 4qo4 4qoc 4ud7 4ue1 4umn 4wt2 4xxb 4zfi 4zgk 4zyc 4zyf 4zyi 5c5a 5hmh 5hmi 5hmk 5j7f 5j7g 5lav 5law 5lay 5laz 5ln2 5mnj 5trf

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5AFG)