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(-) Description

Title :  LYSINE 120-ACETYLATED P53 DNA BINDING DOMAIN IN A COMPLEX WITH THE BAX RESPONSE ELEMENT.
 
Authors :  E. Arbely, R. Vainer
Date :  08 Jul 16  (Deposition) - 27 Jul 16  (Release) - 17 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.92
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Transcription, Acetylation, Transcription Factor, Post-Translational Modification, Tumor Suppressor, Dna Binding Specificity, Apoptosis, Induced Fit, Genetic Code Expansion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Vainer, S. Cohen, A. Shahar, R. Zarivach, E. Arbely
Structural Basis For P53 Lys120-Acetylation-Dependent Dna-Binding Mode.
J. Mol. Biol. V. 428 3013 2016
PubMed-ID: 27338200  |  Reference-DOI: 10.1016/J.JMB.2016.06.009

(-) Compounds

Molecule 1 - CELLULAR TUMOR ANTIGEN P53
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Fragment: UNP RESIDUES 94-291
    Gene: TP53, P53
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ANTIGEN NY-CO-13,PHOSPHOPROTEIN P53,TUMOR SUPPRESSOR P53
 
Molecule 2 - DNA (5'- D(*TP*CP*AP*CP*AP*AP*GP*TP*TP*AP*GP*AP*GP*AP*CP*AP*AP*GP*CP*CP*T)- 3')
    Chains: E
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - DNA (5'- D(*AP*GP*GP*CP*TP*TP*GP*TP*CP*TP*CP*TP*AP*AP*CP*TP*TP*GP*TP*GP*A)- 3')
    Chains: F
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1ALY4Mod. Amino AcidN(6)-ACETYLLYSINE
2ZN4Ligand/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 A 401
2AC2SOFTWARECYS B:176 , HIS B:179 , CYS B:238 , CYS B:242binding site for residue ZN B 301
3AC3SOFTWARECYS C:176 , HIS C:179 , CYS C:238 , CYS C:242binding site for residue ZN C 301
4AC4SOFTWARECYS D:176 , HIS D:179 , CYS D:238 , CYS D:242binding site for residue ZN D 301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Val B:225 -Gly B:226
2Arg B:290 -Lys B:291

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5LGY)

(-) 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:197
                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhh.eee...........eeee....eeee.....eeeeee.........eeeeeeee............hhhhhh.............eee......eee........eeeee..........eeeeeee..............eeeeeeee.....eeeeeeeeeee..hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5lgy A  95 SSVPSQKTYQGSYGFRLGFLHSGTAkSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRK 291
                                   104       114     | 124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       
                                                   120-ALY                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:198
                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........hhhhh.eee...........eeee....eeee.....eeeeee.........eeeeeeee.hhhhhh........................eeee.....eeee......eeeeee..........eeeeeee..............eeeeeeee.....eeeeeeeeeee..hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5lgy B  94 SSSVPSQKTYQGSYGFRLGFLHSGTAkSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRK 291
                                   103       113      |123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283        
                                                    120-ALY                                                                                                                                                                       


Chain C from PDB  Type:PROTEIN  Length:197
                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhh.eee...........eeee....eeee.....eeeeee.........eeeeeeee............hhhhhh.............eeee.....eeee......eeeeee..........eeeeeee..............eeeeeeee.....eeeeeeeeeee..hhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5lgy C  95 SSVPSQKTYQGSYGFRLGFLHSGTAkSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRK 291
                                   104       114     | 124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       
                                                   120-ALY                                                                                                                                                                       


Chain D from PDB  Type:PROTEIN  Length:197
                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhh.eee...........eeee....eeee.....eeeeee.........eeeeeeee..............hhhhh............eee......eeee......eeeeee..........eeeeeee..............eeeeeeee.....eeeeeeeeeee..hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5lgy D  95 SSVPSQKTYQGSYGFRLGFLHSGTAkSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRK 291
                                   104       114     | 124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       
                                                   120-ALY                                                                                                                                                                       


Chain E from PDB  Type:DNA  Length:21
                                                     
                 5lgy E   1 TCACAAGTTAGAGACAAGCCT  21
                                    10        20 


Chain F from PDB  Type:DNA  Length:21
                                                     
                 5lgy F   1 AGGCTTGTCTCTAACTTGTGA  21
                                    10        20
   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 5LGY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (122, 122)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Arg B:290 - Lys B:291   [ RasMol ]  
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  5lgy
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  P53_HUMAN | P04637
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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 5g4n 5g4o 5hou 5hp0 5hpd 5lap 5un8

(-) Related Entries Specified in the PDB File

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