SAXSdb — 1yc5

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1. Protein Identity and Related Structures Protein Identity & Related Structures

NAD-dependent deacetylase

Thermotoga maritima

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–246	Not recorded	Cellular tumor antigen p53 peptide × 1 （Q9NP68） ZN ZINC ION × 1 NCA NICOTINAMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 9.6；293 K；CHES, PEG3350, nicotinamide, pH 9.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.40 Å R-free 0.202

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 1YC5	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2H2D The Structural Basis for Sirtuin Substrate Affinity Deposited 2006-05-18	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–246（246 aa） Fragment：Sir2Tm	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 9.6；298 K；20% PEG 3350, 0.1 M CHES pH 9.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 9.60	Resolution 1.70 Å R-free 0.237
2H2F The Structural basis for Sirtuin Substrate affinity Deposited 2006-05-18	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–246（246 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 9.6；298 K；20% PEG, pH 9.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 9.60	Resolution 2.20 Å R-free 0.246
2H2G The Structural Basis of Sirtuin substrate affinity Deposited 2006-05-18	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–246（246 aa）	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；293.15 K；20% PEG, pH 9.6, VAPOR DIFFUSION, HANGING DROP, pH 7.5, temperature 293.15K	Resolution 1.63 Å R-free 0.226
2H2G The Structural Basis of Sirtuin substrate affinity Deposited 2006-05-18	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–246（246 aa）	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；293.15 K；20% PEG, pH 9.6, VAPOR DIFFUSION, HANGING DROP, pH 7.5, temperature 293.15K	Resolution 1.63 Å R-free 0.226
2H2H The Structural basis of sirtuin substrate specificity Deposited 2006-05-18	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–246（246 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9.5；293.15 K；20 % PEG, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K, pH 9.5	Resolution 2.20 Å R-free 0.239
2H2I The Structural basis of Sirtuin Substrate Affinity Deposited 2006-05-18	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 1–246（246 aa）	Not recorded	ZN ZINC ION × 8 ZPG (2S,5R,8R,11S,14S,17S,21R)-5,8,11,14,17-PENTAMETHYL-4,7,10,13,16,19-HEXAOXADOCOSANE-2,21-DIOL × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.5M (NH4)2SO4, 4% PPG, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.80 Å R-free 0.213
2H4F Sir2-p53 peptide-NAD+ Deposited 2006-05-24	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–246（246 aa）	Not recorded	ZN ZINC ION × 1 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9.6；293 K；CHES, PEG3350, NAD, pH 9.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å R-free 0.228
2H4H Sir2 H116Y mutant-p53 peptide-NAD Deposited 2006-05-24	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–246（246 aa）	Mutation：H116Y	ZN ZINC ION × 1 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9.6；293 K；CHES, PEG 3350, pH9.6, NAD, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.99 Å R-free 0.237
2H4J Sir2-deacetylated peptide (from enzymatic turnover in crystal) Deposited 2006-05-24	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–246（246 aa）	Not recorded	ZN ZINC ION × 1 NCA NICOTINAMIDE × 1 OAD 2'-O-ACETYL ADENOSINE-5-DIPHOSPHORIBOSE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9.6；293 K；CHES, PEG3350, PH9.6, acetylated peptide. Crystals were soaked in cryo + 5mM NAD, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.10 Å R-free 0.246
2H59 Sir2 H116A-deacetylated p53 peptide-3'-o-acetyl ADP ribose Deposited 2006-05-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–246（246 aa） Chain B 1–246（246 aa）	Mutation：H116A Mutation：H116A	ZN ZINC ION × 2 APR ADENOSINE-5-DIPHOSPHORIBOSE × 1 3OD (2S,3S,4R,5S)-2-({[(S)-{[(S)-{[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]OXY}METHYL)-4,5-DIHYDROXYTETRAHYDROFURAN-3-YL ACETATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；PEG 8000, Na-Tartrate:K-Phosphate, NaCl, NAD, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 100K	Resolution 1.90 Å R-free 0.247
3D4B Crystal structure of Sir2Tm in complex with Acetyl p53 peptide and DADMe-NAD+ Deposited 2008-05-14	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–246（246 aa）	Not recorded	ZN ZINC ION × 1 DZD 5'-O-[(R)-{[(R)-{[(3R,4R)-1-(3-carbamoylbenzyl)-4-hydroxypyrrolidin-3-yl]methoxy}(hydroxy)phosphoryl]methyl}(hydroxy)phosphoryl]adenosine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9.5；292 K；PEG 3350, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 1.90 Å R-free 0.229
3D81 Sir2-S-alkylamidate complex crystal structure Deposited 2008-05-22	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–246（246 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9.5；293 K；PEG3350, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.50 Å R-free 0.246
3JR3 Sir2 bound to acetylated peptide Deposited 2009-09-08	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–246（246 aa）	Mutation：H116A	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9.2；298 K；pH 9.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.50 Å R-free 0.228
3PDH Structure of Sir2Tm bound to a propionylated peptide Deposited 2010-10-22	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–246（246 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；Crystals were obtained from 1:1 mix of protein and the well solution (9.5% (w/v) PEG3350, 100 mM CHES buffer), pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.80 Å R-free 0.210
4BUZ SIR2 COMPLEX STRUCTURE MIXTURE OF EX-527 INHIBITOR AND REACTION PRODUCTS OR OF REACTION SUBSTRATES P53 PEPTIDE AND NAD Deposited 2013-06-24	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–246（246 aa）	Not recorded	OCZ (1S)-6-chloro-2,3,4,9-tetrahydro-1H-carbazole-1- carboxamide × 1 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 OAD 2'-O-ACETYL ADENOSINE-5-DIPHOSPHORIBOSE × 1 ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；8.5	Resolution 1.90 Å R-free 0.194
4BV2 CRYSTAL STRUCTURE OF SIR2 IN COMPLEX WITH THE INHIBITOR EX-527, 2'-O-ACETYL-ADP-RIBOSE AND DEACETYLATED P53-PEPTIDE Deposited 2013-06-24	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–246（246 aa）	Not recorded	ZN ZINC ION × 1 OCZ (1S)-6-chloro-2,3,4,9-tetrahydro-1H-carbazole-1- carboxamide × 1 OAD 2'-O-ACETYL ADENOSINE-5-DIPHOSPHORIBOSE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.9；20% PEG 6000, 0.1 M BIS-TRIS PH5.9	Resolution 3.30 Å R-free 0.318
4BV2 CRYSTAL STRUCTURE OF SIR2 IN COMPLEX WITH THE INHIBITOR EX-527, 2'-O-ACETYL-ADP-RIBOSE AND DEACETYLATED P53-PEPTIDE Deposited 2013-06-24	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–246（246 aa）	Not recorded	ZN ZINC ION × 1 OCZ (1S)-6-chloro-2,3,4,9-tetrahydro-1H-carbazole-1- carboxamide × 1 OAD 2'-O-ACETYL ADENOSINE-5-DIPHOSPHORIBOSE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.9；20% PEG 6000, 0.1 M BIS-TRIS PH5.9	Resolution 3.30 Å R-free 0.318
4BV2 CRYSTAL STRUCTURE OF SIR2 IN COMPLEX WITH THE INHIBITOR EX-527, 2'-O-ACETYL-ADP-RIBOSE AND DEACETYLATED P53-PEPTIDE Deposited 2013-06-24	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–246（246 aa）	Not recorded	ZN ZINC ION × 1 OCZ (1S)-6-chloro-2,3,4,9-tetrahydro-1H-carbazole-1- carboxamide × 1 OAD 2'-O-ACETYL ADENOSINE-5-DIPHOSPHORIBOSE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.9；20% PEG 6000, 0.1 M BIS-TRIS PH5.9	Resolution 3.30 Å R-free 0.318
4BV2 CRYSTAL STRUCTURE OF SIR2 IN COMPLEX WITH THE INHIBITOR EX-527, 2'-O-ACETYL-ADP-RIBOSE AND DEACETYLATED P53-PEPTIDE Deposited 2013-06-24	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–246（246 aa）	Not recorded	ZN ZINC ION × 1 OCZ (1S)-6-chloro-2,3,4,9-tetrahydro-1H-carbazole-1- carboxamide × 1 OAD 2'-O-ACETYL ADENOSINE-5-DIPHOSPHORIBOSE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.9；20% PEG 6000, 0.1 M BIS-TRIS PH5.9	Resolution 3.30 Å R-free 0.318

15 other PDB entries and 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NPD_THEMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–246； UniProt 1–246

Cellular tumor antigen p53 peptide

OrganismNot specified

UniProt Q9NP68

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 372–389	Non-standard monomer：Yes (specific site not provided by mmCIF)	NAD-dependent deacetylase × 1 （Q9WYW0） ZN ZINC ION × 1 NCA NICOTINAMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 9.6；293 K；CHES, PEG3350, nicotinamide, pH 9.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.40 Å R-free 0.202

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 1YC5	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2FEJ Solution structure of human p53 DNA binding domain. Deposited 2005-12-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 94–297（204 aa） Fragment：DNA binding domain	Not recorded	ZN ZINC ION × 1	SOLUTION NMR NMR measurement conditions pH 7.1；298 K；Ionic strength (raw mmCIF value) 150 mM；Pressure ambient NMR sample composition 0.4 mM p53 core U-15N,13C, 2H; 25 mM Tris-HCl pH 7.1; 150 mM NaCl; 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 0.3 mM p53 core U-15N,13C, 2H + reverse ILV 13CH3 ; 25 mM Tris-HCl pH 7.1; 150 mM NaCl; 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 0.3 mM p53 core U-15N,13C, 2H + reverse ILV 13CH3 + reverse Tyr ; 25 mM Tris-HCl pH 7.1; 150 mM NaCl; 100% D2O \| 100% D2O NMR sample composition 0.3 mM p53 core U-15N,13C, 2H + Met and Phe (1H); 25 mM Tris-HCl pH 7.1; 150 mM NaCl; 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 0.3 mM p53 core U-15N,13C, 2H + Met and Arg (1H); 25 mM Tris-HCl pH 7.1; 150 mM NaCl; 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 0.4 mM p53 core U-15N,13C, 2H (50%); 25 mM Tris-HCl pH 7.1; 150 mM NaCl; 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 0.4 mM p53 core N/A; 25 mM Tris-HCl pH 7.1; 150 mM NaCl; 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 0.4 mM p53 core N/A; 25 mM Tris-HCl pH 7.1; 150 mM NaCl; 100% D2O \| 100% D2O	Resolution not provided
2H1L The Structure of the Oncoprotein SV40 Large T Antigen and p53 Tumor Suppressor Complex Deposited 2006-05-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain M 92–292（201 aa） Fragment：DNA Binding Domain, residues 92-292 Chain N 92–292（201 aa） Fragment：DNA Binding Domain, residues 92-292 Chain O 92–292（201 aa） Fragment：DNA Binding Domain, residues 92-292 Chain P 92–292（201 aa） Fragment：DNA Binding Domain, residues 92-292 Chain Q 92–292（201 aa） Fragment：DNA Binding Domain, residues 92-292 Chain R 92–292（201 aa） Fragment：DNA Binding Domain, residues 92-292	Not recorded	ZN ZINC ION × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；5.4% PEG 4000, 73mM Mops Buffer, 22mM Lithium Sulfate, pH 6.5, VAPOR DIFFUSION, temperature 298K	Resolution 3.16 Å R-free 0.308
2H1L The Structure of the Oncoprotein SV40 Large T Antigen and p53 Tumor Suppressor Complex Deposited 2006-05-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain S 92–292（201 aa） Fragment：DNA Binding Domain, residues 92-292 Chain T 92–292（201 aa） Fragment：DNA Binding Domain, residues 92-292 Chain U 92–292（201 aa） Fragment：DNA Binding Domain, residues 92-292 Chain V 92–292（201 aa） Fragment：DNA Binding Domain, residues 92-292 Chain W 92–292（201 aa） Fragment：DNA Binding Domain, residues 92-292 Chain X 92–292（201 aa） Fragment：DNA Binding Domain, residues 92-292	Not recorded	ZN ZINC ION × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；5.4% PEG 4000, 73mM Mops Buffer, 22mM Lithium Sulfate, pH 6.5, VAPOR DIFFUSION, temperature 298K	Resolution 3.16 Å R-free 0.308
2H4F Sir2-p53 peptide-NAD+ Deposited 2006-05-24	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 372–389（18 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 1 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9.6；293 K；CHES, PEG3350, NAD, pH 9.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å R-free 0.228
2H4H Sir2 H116Y mutant-p53 peptide-NAD Deposited 2006-05-24	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 372–389（18 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 1 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9.6；293 K；CHES, PEG 3350, pH9.6, NAD, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.99 Å R-free 0.237
2H59 Sir2 H116A-deacetylated p53 peptide-3'-o-acetyl ADP ribose Deposited 2006-05-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 372–389（18 aa） Chain E 372–389（18 aa）	Not recorded	ZN ZINC ION × 2 APR ADENOSINE-5-DIPHOSPHORIBOSE × 1 3OD (2S,3S,4R,5S)-2-({[(S)-{[(S)-{[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]OXY}METHYL)-4,5-DIHYDROXYTETRAHYDROFURAN-3-YL ACETATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；PEG 8000, Na-Tartrate:K-Phosphate, NaCl, NAD, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 100K	Resolution 1.90 Å R-free 0.247

5 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	P53_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–18； UniProt 372–389

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1yc5
Deposition date deposition_date	2004-12-21
Structure title title	Sir2-p53 peptide-nicotinamide
Keywords keywords	sir2, sirtuin, sir2Tm, SirT1, p53, nicotinamide, HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	20.09 Å
Radius of gyration Rg (electron density) rg_electron	18.93 Å
Forward intensity I(0) i0	13063800.00
Molecular weight molecular_weight	27808.0 kDa
Excluded volume excluded_volume	35126 Å³
Envelope volume envelope_volume	40261 Å³
Hydration-shell volume shell_volume	18217 Å³
Envelope diameter envelope_diameter	67.1 Å
Shell Rg shell_rg	24.84 Å
Envelope Rg envelope_rg	19.17 Å
Shape Rg shape_rg	18.87 Å
Total Rg total_rg	20.00 Å
Total atoms total_atoms	1951
Residues n_residues	246
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	65.5 Å
Rg (real space) rg_real	20.09 Å
Rg uncertainty (real space) rg_real_error	0.52 Å
I(0) (real space) i0_real	1.3060e+07
I(0) uncertainty (real space) i0_real_error	1.8690e+05
Rg (reciprocal space) rg_reciprocal	20.09 Å
I(0) (reciprocal space) i0_reciprocal	13060000.0000
Solution quality estimate total_estimate	0.8019
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.4 Å
Skewness Skewness skewness	0.369
Kurtosis Kurtosis kurtosis	-0.283
Angular range angular_range	— – 0.3950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2451000.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.808; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	NAD-dependent deacetylase
Molecular weight formula_weight	27569.8 kDa
EC 编号 ec_number	3.5.1.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2217

MKMKEFLDLLNESRLTVTLTGAGISTPSGIPDFRGPNGIYKKYSQNVFDIDFFYSHPEEFYRFAKEGIFPMLQAKPNLAHVLLAKLEEKGLIEAVITQNIDRLHQRAGSKKVIELHGNVEEYYCVRCEKKYTVEDVIKKLESSDVPLCDDCNSLIRPNIVFFGENLPQDALREAIGLSSRASLMIVLGSSLVVYPAAELPLITVRSGGKLVIVNLGETPFDDIATLKYNMDVVEFARRVMEEGGIS

来源 Source

来源生物 organism	Thermotoga maritima
NCBI Class编号 ncbi_taxonomy_id	2336
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Cellular tumor antigen p53 peptide
Molecular weight formula_weight	2139.5 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

KKGQSTSRHKKLMFKTEG

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	NICOTINAMIDE
Molecular weight formula_weight	122.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	266

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1yc5a1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.31 — DHS-like NAD/FAD-binding domain
Superfamily Superfamily superfamily	c.31.1 — DHS-like NAD/FAD-binding domain
Family Family family	c.31.1.5 — Sir2 family of transcriptional regulators

CATH v4.4 (2 domains)

Domain ID domain_id	1yc5A01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1220 — TPP-binding domain

Domain ID domain_id	1yc5A02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1600 — SIR2/SIRT2 'Small Domain'
Homologous superfamily homologous superfamily	10 — SIR2/SIRT2 'Small Domain'

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8. Citations (1)

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Unit-cell length a length_a	46.100 Å
Unit-cell length b length_b	59.749 Å
Unit-cell length c length_c	106.121 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.400 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.1863
R_work r_work	0.1854
R_free r_free	0.2022

fit	/app/data/saxs_computation/yc/1yc5/1yc5.fit
pddf	/app/data/pr_computation/yc/1yc5/1yc5.pr.out
profile	/app/data/saxs_computation/yc/1yc5/1yc5.dat

Sir2-p53 peptide-nicotinamide

1. Protein Identity and Related Structures Protein Identity & Related Structures

NAD-dependent deacetylase

State in the Current Structure

Other States of the Same Protein in the Database

Cellular tumor antigen p53 peptide

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)