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(-) Description

Title :  CRYSTAL STRUCTURE OF THE P53 CANCER MUTANT Y220C IN COMPLEX WITH A DIFLUORINATED DERIVATIVE OF THE SMALL MOLECULE STABILIZER PHIKAN083
 
Authors :  A. C. Joerger, M. Bauer, R. N. Jones, J. Spencer
Date :  13 May 16  (Deposition) - 22 Jun 16  (Release) - 28 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.35
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Transcription, P53, Cancer, Tumor Suppression, Dna Binding, Cancer Therapy, Small-Molecule Stabilizers, Molecular Chaperone, Fluorine- Protein Interactions (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. R. Bauer, R. N. Jones, M. G. J. Baud, R. Wilcken, F. M. Boeckler, A. R. Fersht, A. C. Joerger, J. Spencer
Harnessing Fluorine-Sulfur Contacts And Multipolar Interactions For The Design Of P53 Mutant Y220C Rescue Drugs.
Acs Chem. Biol. V. 11 2265 2016
PubMed-ID: 27267810  |  Reference-DOI: 10.1021/ACSCHEMBIO.6B00315

(-) Compounds

Molecule 1 - CELLULAR TUMOR ANTIGEN P53
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: DNA-BINDING DOMAIN, RESIDUES 94-312
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: P53, ANTIGEN NY-CO-13, PHOSPHOPROTEIN P53, TUMOR SUPPRESSOR P53

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2O832Ligand/Ion1-[9-(2,2-DIFLUOROETHYL)-9H-CARBAZOL-3-YL]-N-METHYLMETHANAMINE
3ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2O831Ligand/Ion1-[9-(2,2-DIFLUOROETHYL)-9H-CARBAZOL-3-YL]-N-METHYLMETHANAMINE
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2O831Ligand/Ion1-[9-(2,2-DIFLUOROETHYL)-9H-CARBAZOL-3-YL]-N-METHYLMETHANAMINE
3ZN-1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:176 , HIS A:179 , CYS A:238 , CYS A:242BINDING SITE FOR RESIDUE ZN A1293
2AC2SOFTWARECYS B:176 , HIS B:179 , CYS B:238 , CYS B:242BINDING SITE FOR RESIDUE ZN B1291
3AC3SOFTWAREARG B:174 , GLN B:192 , ASP B:207 , PHE B:212 , HIS B:214 , HOH B:2138BINDING SITE FOR RESIDUE GOL B1292
4AC4SOFTWARELEU B:145 , TRP B:146 , VAL B:147 , THR B:150 , CYS B:220 , GLU B:221 , PRO B:222 , PRO B:223 , ASP B:228 , THR B:230BINDING SITE FOR RESIDUE O83 B1293

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5G4N)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5G4N)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5G4N)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5G4N)

(-) Exons   (0, 0)

(no "Exon" information available for 5G4N)

(-) 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:197
                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eee...........eeee....eeee.....eeeeee.........eeeeeeee.hhhhh........hhhhh............eee......eeee......eeeeee..........eeeeeee..............eeeeeeee.....eeeeeeeeeee..hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5g4n A  96 SVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKLFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRAEYLDDRNTFRHSVVVPCEPPEVGSDCTTIHYNYMCYSSCMGGMNRRPILTIITLEDSSGNLLGRDSFEVRVCACPGRDRRTEEENLRKK 292
                                   105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       


Chain B from PDB  Type:PROTEIN  Length:197
                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................eee...........eeee....eeee.....eeeeee.........eeeeeeee..............hhhhh............eee......eeee......eeeeee..........eeeeeee..............eeeeeeee.....eeeeeeeeeee..hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5g4n B  94 SSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKLFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRAEYLDDRNTFRHSVVVPCEPPEVGSDCTTIHYNYMCYSSCMGGMNRRPILTIITLEDSSGNLLGRDSFEVRVCACPGRDRRTEEENLR 290
                                   103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283
   Legend:   → Mismatch (orange background)
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  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 5G4N)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5G4N)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5G4N)

(-) Gene Ontology  (122, 122)

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 Related Entries

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

UniProtKB/Swiss-Prot
        P53_HUMAN | P04637: 1a1u 1aie 1c26 1dt7 1gzh 1h26 1hs5 1jsp 1kzy 1ma3 1olg 1olh 1pes 1pet 1sae 1saf 1sak 1sal 1tsr 1tup 1uol 1xqh 1yc5 1ycq 1ycr 1ycs 2ac0 2ady 2ahi 2ata 2b3g 2bim 2bin 2bio 2bip 2biq 2f1x 2fej 2foj 2foo 2gs0 2h1l 2h2d 2h2f 2h4f 2h4h 2h4j 2h59 2j0z 2j10 2j11 2j1w 2j1x 2j1y 2j1z 2j20 2j21 2k8f 2l14 2ly4 2mej 2mwo 2mwp 2mwy 2mzd 2ocj 2pcx 2ruk 2vuk 2wgx 2x0u 2x0v 2x0w 2xwr 2ybg 2ydr 2z5s 2z5t 3d05 3d06 3d07 3d08 3d09 3d0a 3dab 3dac 3igk 3igl 3kmd 3kz8 3lw1 3oq5 3pdh 3q01 3q05 3q06 3sak 3tg5 3ts8 3zme 4agl 4agm 4agn 4ago 4agp 4agq 4buz 4bv2 4fz3 4hfz 4hje 4ibq 4ibs 4ibt 4ibu 4ibv 4ibw 4iby 4ibz 4ijt 4kvp 4lo9 4loe 4lof 4mzi 4mzr 4qo1 4rp6 4rp7 4x34 4xr8 4zzj 5a7b 5ab9 5aba 5aoi 5aoj 5aok 5aol 5aom 5bua 5ecg 5g4m 5g4o 5hou 5hp0 5hpd 5lap 5lgy 5un8

(-) Related Entries Specified in the PDB File

5g4m CRYSTAL STRUCTURE OF THE P53 CANCER MUTANT Y220C IN COMPLEX WITH A MONOFLUORINATED DERIVATIVE OF THE SMALL MOLECULE STABILIZER PHIKAN083
5g4o CRYSTAL STRUCTURE OF THE P53 CANCER MUTANT Y220C IN COMPLEX WITH A TRIFLUORINATED DERIVATIVE OF THE SMALL MOLECULE STABILIZER PHIKAN083