4IBQ - 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

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

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

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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, 7)

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

Biological Unit 1 (1, 1)

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

Biological Unit 2 (0, 0)

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

Biological Unit 3 (0, 0)

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

Biological Unit 4 (1, 2)

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

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:176 , HIS A:179 , CYS A:238 , CYS A:242	BINDING SITE FOR RESIDUE ZN A 301
2	AC2	SOFTWARE	THR A:150 , PRO A:222 , PRO A:223 , HOH A:460	BINDING SITE FOR RESIDUE ACT A 302
3	AC3	SOFTWARE	CYS B:176 , HIS B:179 , CYS B:238 , CYS B:242	BINDING SITE FOR RESIDUE ZN B 301
4	AC4	SOFTWARE	CYS C:176 , HIS C:179 , CYS C:238 , CYS C:242	BINDING SITE FOR RESIDUE ZN C 301
5	AC5	SOFTWARE	CYS D:176 , HIS D:179 , CYS D:238 , CYS D:242	BINDING SITE FOR RESIDUE ZN D 301
6	AC6	SOFTWARE	ARG A:283 , GLU A:287 , GLY D:154 , ARG D:156 , ARG D:202 , PRO D:219 , HOH D:426 , HOH D:427 , HOH D:531	BINDING SITE FOR RESIDUE EDO D 302
7	AC7	SOFTWARE	GLU D:180 , PRO D:191 , HOH D:455 , HOH D:551	BINDING SITE FOR RESIDUE EDO D 303

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

Asymmetric Unit

No.	Residues
1	Ser D:96	-	Val D:97

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

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

(no "Exon" information available for 4IBQ)

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:192
                                                                                                                                                                                                                                
               SCOP domains d4ibqa_ 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..hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ibq A  97 VPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVCVCACPGRDRRTEEEN 288
                                   106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286

Chain B from PDB  Type:PROTEIN  Length:193
                                                                                                                                                                                                                                 
               SCOP domains d4ibqb_ B: 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............hhhhhh.............eeee.....eeee......eeeeee..........eeeeeee..............eeeeeeee.....eeeeeeeeeee..hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ibq B  96 SVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVCVCACPGRDRRTEEEN 288
                                   105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285

Chain C from PDB  Type:PROTEIN  Length:192
                                                                                                                                                                                                                                
               SCOP domains d4ibqc_ 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.hhhhh......hhhhhh.............eeee.....eeee......eeeeee..........eeeeeee..............eeeeeeee.....eeeeeeeeeee..hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ibq C  97 VPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVCVCACPGRDRRTEEEN 288
                                   106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286

Chain D from PDB  Type:PROTEIN  Length:193
                                                                                                                                                                                                                                 
               SCOP domains d4ibqd_ D: 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.............eeee.....eeee......eeeeee..........eeeeeee..............eeeeeeee.....eeeeeeeeeee..hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ibq D  96 SVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVCVCACPGRDRRTEEEN 288
                                   105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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	d4ibqa_	A:
1b	d4ibqb_	B:
1c	d4ibqc_	C:
1d	d4ibqd_	D:

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

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

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Cis Peptide Bonds
		Ser D:96 - Val D:97	[ RasMol ]

Biological Units
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		Biological Unit 3	[ Jena3D ]
		Biological Unit 4	[ Jena3D ]

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 7)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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