Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
(-)Biological Unit 3
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)

(-) Description

Title :  THE 2.3A CRYSTAL STRUCTURE OF HUMANIZED XENOPUS MDM2 WITH RO5545353
 
Authors :  B. J. Graves, C. Lukacs, C. A. Janson
Date :  28 Jul 13  (Deposition) - 02 Jul 14  (Release) - 02 Jul 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.32
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Mdm2, E3 Ubiquitin Ligase, P53, Nucleus, Ligase-Ligase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Zhang, X. J. Chu, J. J. Liu, Q. Ding, J. Zhang, D. Bartkovitz, N. Jiang P. Karnachi, S. S. So, C. Tovar, Z. M. Filipovic, B. Higgins, K. Glenn, K. Packman, L. Vassilev, B. Graves
Discovery Of Potent And Orally Active P53-Mdm2 Inhibitors Ro5353 And Ro2468 For Potential Clinical Development.
Acs Med. Chem. Lett. V. 5 124 2014
PubMed-ID: 24900784  |  Reference-DOI: 10.1021/ML400359Z

(-) Compounds

Molecule 1 - E3 UBIQUITIN-PROTEIN LIGASE MDM2
    Chains: A, B, C
    EC Number: 6.3.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PUBS 520
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL DOMAIN (UNP RESIDUES 21-105)
    Gene: MDM2
    Mutation: YES
    Organism Common: CLAWED FROG,COMMON PLATANNA,PLATANNA
    Organism Scientific: XENOPUS LAEVIS
    Organism Taxid: 8355
    Synonym: DOUBLE MINUTE 2 PROTEIN, XDM2, P53-BINDING PROTEIN MDM2

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
120W3Ligand/Ion(2S,3R,4R,5R)-N-(4-CARBAMOYL-2-METHOXYPHENYL)-2'-CHLORO-4-(3-CHLORO-2-FLUOROPHENYL)-2-(2,2-DIMETHYLPROPYL)-5'-OXO-4',5'-DIHYDROSPIRO[PYRROLIDINE-3,6'-THIENO[3,2-B]PYRROLE]-5-CARBOXAMIDE
2SO43Ligand/IonSULFATE ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
120W1Ligand/Ion(2S,3R,4R,5R)-N-(4-CARBAMOYL-2-METHOXYPHENYL)-2'-CHLORO-4-(3-CHLORO-2-FLUOROPHENYL)-2-(2,2-DIMETHYLPROPYL)-5'-OXO-4',5'-DIHYDROSPIRO[PYRROLIDINE-3,6'-THIENO[3,2-B]PYRROLE]-5-CARBOXAMIDE
2SO43Ligand/IonSULFATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
120W1Ligand/Ion(2S,3R,4R,5R)-N-(4-CARBAMOYL-2-METHOXYPHENYL)-2'-CHLORO-4-(3-CHLORO-2-FLUOROPHENYL)-2-(2,2-DIMETHYLPROPYL)-5'-OXO-4',5'-DIHYDROSPIRO[PYRROLIDINE-3,6'-THIENO[3,2-B]PYRROLE]-5-CARBOXAMIDE
2SO4-1Ligand/IonSULFATE ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
120W1Ligand/Ion(2S,3R,4R,5R)-N-(4-CARBAMOYL-2-METHOXYPHENYL)-2'-CHLORO-4-(3-CHLORO-2-FLUOROPHENYL)-2-(2,2-DIMETHYLPROPYL)-5'-OXO-4',5'-DIHYDROSPIRO[PYRROLIDINE-3,6'-THIENO[3,2-B]PYRROLE]-5-CARBOXAMIDE
2SO4-1Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:50 , HIS A:69 , PHE A:82 , VAL A:89 , LYS A:90 , HIS A:92 , ILE A:95 , TYR A:96 , HOH A:314 , LYS C:90 , 20W C:201 , HOH C:308BINDING SITE FOR RESIDUE 20W A 201
2AC2SOFTWAREHIS A:92 , TYR A:96 , HOH A:306 , HOH A:317 , LYS C:90 , GLU C:91 , HIS C:92 , ARG C:93BINDING SITE FOR RESIDUE SO4 A 202
3AC3SOFTWARELYS A:90 , GLU A:91 , HIS A:92 , ARG A:93 , HOH A:307 , HOH A:315 , HIS C:92 , TYR C:96BINDING SITE FOR RESIDUE SO4 A 203
4AC4SOFTWAREPRO A:28 , LEU A:29 , PRO B:28 , LEU B:29 , PRO C:28 , LEU C:29BINDING SITE FOR RESIDUE SO4 A 204
5AC5SOFTWARELEU B:50 , MET B:58 , TYR B:63 , GLU B:65 , GLN B:68 , VAL B:89 , LYS B:90 , HIS B:92 , ILE B:95 , TYR B:96BINDING SITE FOR RESIDUE 20W B 201
6AC6SOFTWARE20W A:201 , HOH A:314 , LEU C:50 , MET C:58 , HIS C:69 , VAL C:89 , LYS C:90 , HIS C:92 , TYR C:96 , HOH C:311BINDING SITE FOR RESIDUE 20W C 201

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4LWV)

(-) 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:85
                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eehhhhhhhhhhh.......hhhhhhhhhhhhhhhh..ee.....eee...hhhhhhhh..eee..hhhhhhhhhhh.eee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------- Transcript
                 4lwv A  21 EKLVQPTPLLLSLLKSAGAQKETFTMKEVLYHLGQYIMAKQLYDEKQQHIVHCSNDPLGELFGVQEFSVKEHRRIYAMISRNLVS 105
                                    30        40        50        60        70        80        90       100     


Chain B from PDB  Type:PROTEIN  Length:85
                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee..hhhhhhhhhhh......eehhhhhhhhhhhhhhhh........eee...hhhhhhhh..eee..hhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------- Transcript
                 4lwv B  21 EKLVQPTPLLLSLLKSAGAQKETFTMKEVLYHLGQYIMAKQLYDEKQQHIVHCSNDPLGELFGVQEFSVKEHRRIYAMISRNLVS 105
                                    30        40        50        60        70        80        90       100     


Chain C from PDB  Type:PROTEIN  Length:85
                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhh.......hhhhhhhhhhhhhhhhh........eee...hhhhhhhh..eee..hhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------- Transcript
                 4lwv C  21 EKLVQPTPLLLSLLKSAGAQKETFTMKEVLYHLGQYIMAKQLYDEKQQHIVHCSNDPLGELFGVQEFSVKEHRRIYAMISRNLVS 105
                                    30        40        50        60        70        80        90       100
   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 4LWV)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    20W  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4lwv)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format | Biol. Unit 3 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4lwv
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  MDM2_XENLA | P56273
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  6.3.2.-
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  MDM2_XENLA | P56273
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        MDM2_XENLA | P56273: 1ttv 1ycq 4ipf 4j3e 4j74 4j7d 4j7e 4jrg 4jsc 4lwt 4lwu

(-) Related Entries Specified in the PDB File

4lwt 4lwu