4IBZ - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   HUMAN P53 CORE DOMAIN WITH HOT SPOT MUTATION R273C AND SECOND-SITE SUPPRESSOR MUTATION T284R

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 :   1.92

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)

Keywords :   Metal-Binding, Loop-Sheet-Helix Motif, Transcription, Activator, Anti-Oncogene, Apoptosis, Cell Cycle, Disease Mutation, Rescue Mutation, Tumor Suppressor, Dna Binding Protein (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

Molecule 1 - CELLULAR TUMOR ANTIGEN P53
	Chains	:	A, B, C, D
	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

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:				D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 25)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	EDO	19	Ligand/Ion	1,2-ETHANEDIOL
3	ZN	4	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	ACT	-1	Ligand/Ion	ACETATE ION
2	EDO	4	Ligand/Ion	1,2-ETHANEDIOL
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (2, 6)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	EDO	5	Ligand/Ion	1,2-ETHANEDIOL
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (1, 4)

No.	Name	Count	Type	Full Name
1	ACT	-1	Ligand/Ion	ACETATE ION
2	EDO	4	Ligand/Ion	1,2-ETHANEDIOL
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 4 (2, 7)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	EDO	6	Ligand/Ion	1,2-ETHANEDIOL
3	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (25, 25)

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	THR A:170 , VAL A:172	BINDING SITE FOR RESIDUE EDO A 302
03	AC3	SOFTWARE	ARG A:158 , ALA A:159 , MET A:160 , ILE A:254 , THR A:256 , HOH A:433 , HOH A:439	BINDING SITE FOR RESIDUE EDO A 303
04	AC4	SOFTWARE	ASP A:186 , ARG A:196 , VAL A:197 , GLU A:198 , ASN A:235 , MET A:237	BINDING SITE FOR RESIDUE EDO A 304
05	AC5	SOFTWARE	THR A:102 , HOH A:555	BINDING SITE FOR RESIDUE EDO A 305
06	AC6	SOFTWARE	CYS B:176 , HIS B:179 , CYS B:238 , CYS B:242	BINDING SITE FOR RESIDUE ZN B 301
07	AC7	SOFTWARE	SER B:260 , SER B:261 , HOH B:529 , ALA D:119 , LYS D:120 , HOH D:435	BINDING SITE FOR RESIDUE EDO B 302
08	AC8	SOFTWARE	ASP B:207 , HOH B:470 , HOH B:506 , LEU D:114 , HIS D:115	BINDING SITE FOR RESIDUE EDO B 303
09	AC9	SOFTWARE	PRO B:190 , PRO B:191 , GLN B:192 , HIS B:193 , ASP B:207 , HIS B:214 , HOH B:456 , HIS D:115	BINDING SITE FOR RESIDUE EDO B 304
10	BC1	SOFTWARE	PHE B:113 , HIS B:115 , GLN B:144 , HOH B:541 , EDO D:302 , EDO D:306	BINDING SITE FOR RESIDUE EDO B 305
11	BC2	SOFTWARE	MET B:160 , LEU B:206 , ASP B:208 , THR B:211 , ARG B:213 , HIS B:214 , SER B:215 , HOH B:503 , HOH B:562	BINDING SITE FOR RESIDUE EDO B 306
12	BC3	SOFTWARE	ARG B:110 , HOH B:505 , EDO D:302 , EDO D:307	BINDING SITE FOR RESIDUE ACT B 307
13	BC4	SOFTWARE	CYS C:176 , HIS C:179 , CYS C:238 , CYS C:242	BINDING SITE FOR RESIDUE ZN C 301
14	BC5	SOFTWARE	PRO C:98 , ARG C:158 , MET C:160 , ILE C:254 , THR C:256 , HOH C:437	BINDING SITE FOR RESIDUE EDO C 302
15	BC6	SOFTWARE	LEU A:114 , HIS A:115 , SER A:116 , ASP C:207 , ARG C:209 , HOH C:496	BINDING SITE FOR RESIDUE EDO C 303
16	BC7	SOFTWARE	ALA A:119 , SER C:261 , GLY C:262 , HOH C:467	BINDING SITE FOR RESIDUE EDO C 304
17	BC8	SOFTWARE	ARG C:209 , ASN C:210	BINDING SITE FOR RESIDUE EDO C 305
18	BC9	SOFTWARE	CYS D:176 , HIS D:179 , CYS D:238 , CYS D:242	BINDING SITE FOR RESIDUE ZN D 301
19	CC1	SOFTWARE	HIS B:115 , TRP B:146 , EDO B:305 , ACT B:307 , PRO D:191 , GLN D:192 , EDO D:307	BINDING SITE FOR RESIDUE EDO D 302
20	CC2	SOFTWARE	LEU D:114 , SER D:116 , CYS D:124 , THR D:125 , TYR D:126 , HOH D:434 , HOH D:527	BINDING SITE FOR RESIDUE EDO D 303
21	CC3	SOFTWARE	SER D:240 , ARG D:248 , CYS D:273	BINDING SITE FOR RESIDUE EDO D 304
22	CC4	SOFTWARE	MET D:160 , LEU D:206 , ASP D:208 , THR D:211 , ARG D:213 , HIS D:214 , SER D:215 , HOH D:442 , HOH D:520	BINDING SITE FOR RESIDUE EDO D 305
23	CC5	SOFTWARE	LEU B:114 , HIS B:115 , EDO B:305 , ASP D:207 , HOH D:432	BINDING SITE FOR RESIDUE EDO D 306
24	CC6	SOFTWARE	TRP B:146 , ACT B:307 , GLU D:180 , PRO D:191 , EDO D:302 , HOH D:526 , HOH D:541	BINDING SITE FOR RESIDUE EDO D 307
25	CC7	SOFTWARE	GLY D:187 , HOH D:450 , HOH D:482	BINDING SITE FOR RESIDUE ACT D 308

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

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

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

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

(no "Exon" information available for 4IBZ)

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:193
                                                                                                                                                                                                                                 
               SCOP domains d4ibza_ 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.............eee......eeee......eeeeee..........eeeeeee..............eeeeeeee.....eeeeeeeeeee..hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ibz A  96 SVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVCVCACPGRDRRREEEN 288
                                   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:192
                                                                                                                                                                                                                                
               SCOP domains d4ibzb_ B: p53 tumor suppressor, DNA-binding domain                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .............eee...........eeee....eeee.....eeeeee.........eeeeeeee............hhhhhh.............eee......eeee......eeeeee..........eeeeeee..............eeeeeeee.....eeeeeeeeeee..hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ibz B  97 VPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVCVCACPGRDRRREEEN 288
                                   106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286

Chain C from PDB  Type:PROTEIN  Length:192
                                                                                                                                                                                                                                
               SCOP domains d4ibzc_ C: p53 tumor suppressor, DNA-binding domain                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..............eee...........eeee....eeee.....eeeeee.........eeeeeeee............hhhhhh...........eee......eeee......eeeeee..........eeeeeee..............eeeeeeee.....eeeeeeeeeee..hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ibz C  96 SVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVCVCACPGRDRRREEENL 289
                                   105       115       125       135       145       155       165       175      |187       197       207       217       227       237       247       257       267       277       287  
                                                                                                                182|                                                                                                        
                                                                                                                 185

Chain D from PDB  Type:PROTEIN  Length:192
                                                                                                                                                                                                                                
               SCOP domains d4ibzd_ D: p53 tumor suppressor, DNA-binding domain                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........hhhhh.eee...........eeee....eeee.....eeeeee.........eeeeeeee............hhhhhhh............eeee.....eeee......eeeeee.........eeeeeee..............eeeeeeee.....eeeeeeeeeee..hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ibz D  96 SVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVCVCACPGRDRRREEEN 288
                                   105       115       125       135       145       155       165       175       185       195       205       215       225|      236       246       256       266       276       286  
                                                                                                                                                           225|                                                             
                                                                                                                                                            227

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	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 '\|'

Asymmetric Unit

Classes(

)

Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: All beta proteins (24004)

Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f (364)

Superfamily: p53-like transcription factors (153)

Family: p53 DNA-binding domain-like (80)

Protein domain: p53 tumor suppressor, DNA-binding domain (33)

Human (Homo sapiens) [TaxId: 9606] (32)

1a	d4ibza_	A:
1b	d4ibzb_	B:
1c	d4ibzc_	C:
1d	d4ibzd_	D:

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

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

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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Description

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Ligands, Modified Residues, Ions (3, 25)

Sites (25, 25)

SS Bonds (0, 0)

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