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(-) Description

Title :  CRYSTAL STRUCTURE OF P53 CORE DOMAIN IN COMPLEX WITH DNA
 
Authors :  Y. Chen, L. Chen
Date :  12 Oct 12  (Deposition) - 17 Jul 13  (Release) - 09 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.91
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Tumor Suppressor, Transcription-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Chen, X. Zhang, A. C. Dantas Machado, Y. Ding, Z. Chen, P. Z. Qin, R. Rohs, L. Chen
Structure Of P53 Binding To The Bax Response Element Reveal Dna Unwinding And Compression To Accommodate Base-Pair Insertion.
Nucleic Acids Res. V. 41 8368 2013
PubMed-ID: 23836939  |  Reference-DOI: 10.1093/NAR/GKT584

(-) Compounds

Molecule 1 - CELLULAR TUMOR ANTIGEN P53
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 92-291
    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
    Other Details: THIS SEQUENCE OCCURS NATURALLY IN HUMANS
    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
    Other Details: THIS SEQUENCE OCCURS NATURALLY IN HUMANS
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1ZN4Ligand/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 301
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 4HJE)

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4HJE)

(-) 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:200
                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................eee...........eeee....eeee.....eeeeee.........eeeeeeee.hhhhh......hhhhhhh............eee......eeee......eeeeee..........eeeeeee..............eeeeeeee.....eeeeeeeeeee..hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hje A  92 PLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRK 291
                                   101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291


Chain B from PDB  Type:PROTEIN  Length:200
                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................eee...........eeee....eeee.....eeeeee.........eeeeeeee.hhhhh......hhhhhhh............eee......eeee......eeeeee..........eeeeeee..............eeeeeeee.....eeeeeeeeeee..hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hje B  92 PLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRK 291
                                   101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291


Chain C from PDB  Type:PROTEIN  Length:200
                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................eee...........eeee....eeee.....eeeeee.........eeeeeeee.hhhhh......hhhhhhh............eee......eeee......eeeeee..........eeeeeee..............eeeeeeee.....eeeeeeeeeee..hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hje C  92 PLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRK 291
                                   101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291


Chain D from PDB  Type:PROTEIN  Length:200
                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................eee...........eeee....eeee.....eeeeee.........eeeeeeee.hhhhh......hhhhhhh............eee......eeee......eeeeee..........eeeeeee..............eeeeeeee.....eeeeeeeeeee..hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hje D  92 PLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRK 291
                                   101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291


Chain E from PDB  Type:DNA  Length:21
                                                     
                 4hje E   1 TCACAAGTTAGAGACAAGCCT  21
                                    10        20 


Chain F from PDB  Type:DNA  Length:21
                                                     
                 4hje 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 4HJE)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (122, 122)

Asymmetric/Biological Unit(hide GO term definitions)

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  4hje
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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 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 5lgy 5un8

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4HJE)