4IBW - JenaLib

Title :   HUMAN P53 CORE DOMAIN WITH HOT SPOT MUTATION R273H AND SECOND-SITE SUPPRESSOR MUTATION T284R IN SEQUENCE-SPECIFIC COMPLEX WITH DNA

Authors :   A. Eldar, H. Rozenberg, Y. Diskin-Posner, Z. Shakked

Date :   09 Dec 12 (Deposition) - 14 Aug 13 (Release) - 23 Oct 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.79

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (2x)

Keywords :   Metal-Binding, Loop-Sheet-Helix Motif, Transcription, Activator, Anti-Oncogene, Apoptosis, Cell Cycle, Disease Mutation, Rescue Mutation, Tumor Suppressor, Dna Binding Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Eldar, H. Rozenberg, Y. Diskin-Posner, R. Rohs, Z. Shakked
Structural Studies Of P53 Inactivation By Dna-Contact Mutations And Its Rescue By Suppressor Mutations Via Alternative Protein-Dna Interactions.
Nucleic Acids Res. V. 41 8748 2013
PubMed-ID: 23863845 | Reference-DOI: 10.1093/NAR/GKT630

Compounds

Molecule 1 - CELLULAR TUMOR ANTIGEN P53
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-27-B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	DNA BINDING DOMAIN
	Gene	:	P53, TP53
	Mutation	:	YES
	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(CPGPGPGPCPAPTPGPCPCPCPG)-3')*
	Chains	:	B
	Engineered	:	YES
	Synthetic	:	YES

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 18)

Sites (18, 18)

Asymmetric Unit (18, 18)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	CYS A:176 , HIS A:179 , CYS A:238 , CYS A:242	BINDING SITE FOR RESIDUE ZN A 301
02	AC2	SOFTWARE	SER A:95 , THR A:231 , HIS A:233 , HOH A:659	BINDING SITE FOR RESIDUE EDO A 302
03	AC3	SOFTWARE	ARG A:110 , ASP A:148 , ASP A:208 , ASN A:210 , EDO A:306 , HOH A:465 , HOH A:559 , HOH A:658 , HOH A:683	BINDING SITE FOR RESIDUE EDO A 303
04	AC4	SOFTWARE	GLU A:224 , VAL A:225 , HOH A:518 , HOH A:633 , HOH A:673	BINDING SITE FOR RESIDUE EDO A 304
05	AC5	SOFTWARE	ARG A:110 , LEU A:111 , TRP A:146 , HOH A:555 , HOH A:607	BINDING SITE FOR RESIDUE EDO A 305
06	AC6	SOFTWARE	ARG A:110 , TRP A:146 , VAL A:147 , ASP A:148 , ASP A:228 , EDO A:303 , HOH A:456 , HOH A:575 , HOH A:658 , HOH A:686	BINDING SITE FOR RESIDUE EDO A 306
07	AC7	SOFTWARE	LEU A:114 , SER A:166 , MET A:169 , HIS A:233 , HOH A:498 , HOH A:536	BINDING SITE FOR RESIDUE EDO A 307
08	AC8	SOFTWARE	PHE A:113 , LEU A:114 , HIS A:115 , TYR A:126 , PRO A:128 , ARG A:282 , HOH A:466 , HOH A:477 , HOH A:532 , HOH A:622	BINDING SITE FOR RESIDUE EDO A 308
09	AC9	SOFTWARE	LYS A:132 , SER A:240 , ARG A:248 , PRO A:250 , GLU A:271 , VAL A:272 , HIS A:273 , HOH A:507	BINDING SITE FOR RESIDUE EDO A 309
10	BC1	SOFTWARE	ASP A:186 , ARG A:196 , ASN A:235 , HOH A:669	BINDING SITE FOR RESIDUE EDO A 310
11	BC2	SOFTWARE	ALA A:138 , LYS A:139 , THR A:140 , GLN A:167 , GLU A:198 , ASN A:235 , HOH A:655	BINDING SITE FOR RESIDUE EDO A 311
12	BC3	SOFTWARE	CYS A:229 , THR A:231 , HOH A:470 , HOH A:548	BINDING SITE FOR RESIDUE EDO A 312
13	BC4	SOFTWARE	SER A:94 , SER A:95 , SER A:96 , ASN A:200 , LEU A:201 , EDO A:315 , HOH A:594 , HOH A:679	BINDING SITE FOR RESIDUE EDO A 313
14	BC5	SOFTWARE	LYS A:120 , ARG A:280 , ARG A:283 , HOH A:464 , HOH A:547 , DG B:3 , HOH B:227	BINDING SITE FOR RESIDUE EDO A 314
15	BC6	SOFTWARE	SER A:95 , GLU A:221 , THR A:230 , THR A:231 , EDO A:313 , HOH A:492 , HOH A:634	BINDING SITE FOR RESIDUE EDO A 315
16	BC7	SOFTWARE	ARG A:283 , GLU A:286 , GLU A:287	BINDING SITE FOR RESIDUE EDO A 316
17	BC8	SOFTWARE	ARG A:248 , DT B:7 , DG B:8 , EDO B:102 , HOH B:241	BINDING SITE FOR RESIDUE EDO B 101
18	BC9	SOFTWARE	SER A:241 , ARG A:248 , DC B:9 , EDO B:101 , HOH B:213 , HOH B:219 , HOH B:223	BINDING SITE FOR RESIDUE EDO B 102

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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

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Chain A from PDB  Type:PROTEIN  Length:197
                                                                                                                                                                                                                                     
               SCOP domains d4ibwa_ A: p53 tumor suppressor, DNA-binding domain                                                                                                                                                   SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................eee...........eeee....eeee.....eeeeee.........eeeeeeee.hhhhh......hhhhhh..........eeee.....eeee......eeeeee..........eeeeeee..............eeeeeeee.....eeeeeeeeeee..hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ibw A  94 SSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVHVCACPGRDRRREEENLRKKG 293
                                   103       113       123       133       143       153       163       173       186       196       206       216       226       236       246       256       266       276       286       
                                                                                                                  182|                                                                                                           
                                                                                                                   186

Chain B from PDB  Type:DNA  Length:12
                                            
                 4ibw B   1 CGGGCATGCCCG  12
                                    10

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 (1, 1)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (122, 122)

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