SAXSdb — 2h2i

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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 homooligomer Homooligomer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count	Chain A； UniProt 1–246	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

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 2H2I	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1YC5 Sir2-p53 peptide-nicotinamide Deposited 2004-12-21	Different oligomeric state 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	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
2H2D The Structural Basis for Sirtuin Substrate Affinity Deposited 2006-05-18	Different construct Different oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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
2H4F Sir2-p53 peptide-NAD+ Deposited 2006-05-24	Different oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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

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	2h2i
Deposition date deposition_date	2006-05-18
Structure title title	The Structural basis of Sirtuin Substrate Affinity
Keywords keywords	Sir2Tm-PPG, 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	20.32 Å
Radius of gyration Rg (electron density) rg_electron	19.20 Å
Forward intensity I(0) i0	12873600.00
Molecular weight molecular_weight	27805.0 kDa
Excluded volume excluded_volume	35243 Å³
Envelope volume envelope_volume	40015 Å³
Hydration-shell volume shell_volume	18004 Å³
Envelope diameter envelope_diameter	67.1 Å
Shell Rg shell_rg	24.82 Å
Envelope Rg envelope_rg	19.35 Å
Shape Rg shape_rg	19.15 Å
Total Rg total_rg	20.21 Å
Total atoms total_atoms	1951
Residues n_residues	244
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	65.0 Å
Rg (real space) rg_real	20.33 Å
Rg uncertainty (real space) rg_real_error	0.41 Å
I(0) (real space) i0_real	1.2870e+07
I(0) uncertainty (real space) i0_real_error	1.5890e+05
Rg (reciprocal space) rg_reciprocal	20.33 Å
I(0) (reciprocal space) i0_reciprocal	12870000.0000
Solution quality estimate total_estimate	0.8016
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	23.2 Å
Skewness Skewness skewness	0.380
Kurtosis Kurtosis kurtosis	-0.333
Angular range angular_range	— – 0.3900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2743000.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.809; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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	2176

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 non-polymer

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

Entity 3 Entity 3 non-polymer

Description description	(2S,5R,8R,11S,14S,17S,21R)-5,8,11,14,17-PENTAMETHYL-4,7,10,13,16,19-HEXAOXADOCOSANE-2,21-DIOL
Molecular weight formula_weight	424.6 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	208

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2h2ia_
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.31.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	2h2iA01
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	2h2iA02
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	133.107 Å
Unit-cell length b length_b	133.107 Å
Unit-cell length c length_c	133.107 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	24

Space group space_group	P 4 3 2
Space-group number int_tables_number	207
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	129.100 Å
R factor r_factor	0.1877
R_work r_work	0.1863
R_free r_free	0.2125

fit	/app/data/saxs_computation/h2/2h2i/2h2i.fit
pddf	/app/data/pr_computation/h2/2h2i/2h2i.pr.out
profile	/app/data/saxs_computation/h2/2h2i/2h2i.dat

The Structural basis of Sirtuin Substrate Affinity

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

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