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(-) Description

Title :  CRYSTAL STRUCTURE OF MDM2 (17-111) IN COMPLEX WITH COMPOUND 29 (AM-8553)
 
Authors :  X. Huang
Date :  20 Apr 12  (Deposition) - 23 May 12  (Release) - 02 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,C,E
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  C  (1x)
Biol. Unit 3:  E  (1x)
Keywords :  Mdm2, P53, Protein Protein Interaction, Ligase-Ligase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Rew, D. Sun, F. Gonzalez-Lopez De Turiso, M. D. Bartberger, H. P. Beck, J. Canon, A. Chen, D. Chow, J. Deignan, B. M. Fox, D. Gustin, X. Huang, M. Jiang, X. Jiao, L. Jin, F. Kayser, D. J. Kopecky, Y. Li, M. C. Lo, A. M. Long, K. Michelsen, J. D. Oliner, T. Osgood, M. Ragains, A. Y. Saiki, S. Schneider, M. Toteva, P. Yakowec, X. Yan, Q. Ye, D. Yu, X. Zhao, J. Zhou, J. C. Medina, S. H. Olson
Structure-Based Design Of Novel Inhibitors Of The Mdm2-P53 Interaction.
J. Med. Chem. V. 55 4936 2012
PubMed-ID: 22524527  |  Reference-DOI: 10.1021/JM300354J

(-) Compounds

Molecule 1 - E3 UBIQUITIN-PROTEIN LIGASE MDM2
    Chains: A, C, E
    EC Number: 6.3.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 17-111
    Gene: MDM2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DOUBLE MINUTE 2 PROTEIN, HDM2, ONCOPROTEIN MDM2, P53-BINDING PROTEIN MDM2

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ACE
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  C 
Biological Unit 3 (1x):   E

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
10R33Ligand/Ion{(3R,5R,6S)-5-(3-CHLOROPHENYL)-6-(4-CHLOROPHENYL)-1-[(2S,3S)-2-HYDROXYPENTAN-3-YL]-3-METHYL-2-OXOPIPERIDIN-3-YL}ACETIC ACID
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
10R31Ligand/Ion{(3R,5R,6S)-5-(3-CHLOROPHENYL)-6-(4-CHLOROPHENYL)-1-[(2S,3S)-2-HYDROXYPENTAN-3-YL]-3-METHYL-2-OXOPIPERIDIN-3-YL}ACETIC ACID
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
10R31Ligand/Ion{(3R,5R,6S)-5-(3-CHLOROPHENYL)-6-(4-CHLOROPHENYL)-1-[(2S,3S)-2-HYDROXYPENTAN-3-YL]-3-METHYL-2-OXOPIPERIDIN-3-YL}ACETIC ACID
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
10R31Ligand/Ion{(3R,5R,6S)-5-(3-CHLOROPHENYL)-6-(4-CHLOROPHENYL)-1-[(2S,3S)-2-HYDROXYPENTAN-3-YL]-3-METHYL-2-OXOPIPERIDIN-3-YL}ACETIC ACID

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:54 , ILE A:61 , TYR A:67 , VAL A:93 , LYS A:94 , HIS A:96 , ILE A:99 , TYR A:100 , HOH A:325 , HOH A:335BINDING SITE FOR RESIDUE 0R3 A 201
2AC2SOFTWAREARG A:97 , LEU C:54 , GLY C:58 , VAL C:93 , LYS C:94 , HIS C:96 , ILE C:99 , HOH C:323BINDING SITE FOR RESIDUE 0R3 C 201
3AC3SOFTWARELEU E:54 , ILE E:61 , VAL E:93 , LYS E:94 , HIS E:96 , TYR E:100BINDING SITE FOR RESIDUE 0R3 E 201

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ERF)

(-) 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:92
                                                                                                                            
               SCOP domains d4erfa_ A: MDM2                                                                              SCOP domains
               CATH domains -------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh.eeeehhhhhhhhh........eehhhhhhhhhhhhhhh.........eee...hhhhhhhh..eee..hhhhhhhhhhh.eee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                 4erf A  19 IPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLVVV 110
                                    28        38        48        58        68        78        88        98       108  


Chain C from PDB  Type:PROTEIN  Length:93
                                                                                                                             
               SCOP domains d4erfc_ C: MDM2                                                                               SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh.eeeehhhhhhhhhh.......eehhhhhhhhhhhhhhh.........eee...hhhhhhhh..eee..hhhhhhhhhhh.eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 4erf C  18 QIPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLVVV 110
                                    27        37        47        57        67        77        87        97       107   


Chain E from PDB  Type:PROTEIN  Length:93
                                                                                                                             
               SCOP domains d4erfe_ E: MDM2                                                                               SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh.eeeehhhhhhhhhh.......eehhhhhhhhhhhhhhh.........eee...hhhhhhhh..eee..hhhhhhhhhhh.eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 4erf E  18 QIPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLVVV 110
                                    27        37        47        57        67        77        87        97       107
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (1, 3)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (83, 83)

Asymmetric Unit(hide GO term definitions)

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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 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 5afg 5c5a 5hmh 5hmi 5hmk 5j7f 5j7g 5lav 5law 5lay 5laz 5ln2 5mnj 5trf

(-) Related Entries Specified in the PDB File

4ere