SAXSdb — 1pt9

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

NAD(P) transhydrogenase, mitochondrial

OrganismNot specified

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 880–1086	Fragment：residues 880-1086	SO4 SULFATE ION × 1 TAP 7-THIONICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；ammonium sulfate, peg 400, glycerol, pH 7.00, VAPOR DIFFUSION, SITTING DROP, temperature 100K	Resolution 2.42 Å R-free 0.278
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 880–1086	Fragment：residues 880-1086	SO4 SULFATE ION × 1 TAP 7-THIONICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；ammonium sulfate, peg 400, glycerol, pH 7.00, VAPOR DIFFUSION, SITTING DROP, temperature 100K	Resolution 2.42 Å R-free 0.278
3	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 880–1086 Chain B； UniProt 880–1086	Fragment：residues 880-1086	SO4 SULFATE ION × 4 TAP 7-THIONICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 4 GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；ammonium sulfate, peg 400, glycerol, pH 7.00, VAPOR DIFFUSION, SITTING DROP, temperature 100K	Resolution 2.42 Å R-free 0.278
4	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 880–1086 Chain B； UniProt 880–1086	Fragment：residues 880-1086	SO4 SULFATE ION × 2 TAP 7-THIONICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；ammonium sulfate, peg 400, glycerol, pH 7.00, VAPOR DIFFUSION, SITTING DROP, temperature 100K	Resolution 2.42 Å R-free 0.278
5	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 880–1086	Fragment：residues 880-1086	SO4 SULFATE ION × 2 TAP 7-THIONICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；ammonium sulfate, peg 400, glycerol, pH 7.00, VAPOR DIFFUSION, SITTING DROP, temperature 100K	Resolution 2.42 Å R-free 0.278
6	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 880–1086	Fragment：residues 880-1086	SO4 SULFATE ION × 2 TAP 7-THIONICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；ammonium sulfate, peg 400, glycerol, pH 7.00, VAPOR DIFFUSION, SITTING DROP, temperature 100K	Resolution 2.42 Å R-free 0.278

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 1PT9	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1DJL THE CRYSTAL STRUCTURE OF HUMAN TRANSHYDROGENASE DOMAIN III WITH BOUND NADP Deposited 1999-12-03	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 880–1086（207 aa） Fragment：RESIDUES 837-1086 Chain B 880–1086（207 aa） Fragment：RESIDUES 837-1086	Not recorded	SO4 SULFATE ION × 2 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；AMMONIUM SULPHATE, MOPS, DIOXANE, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.00 Å R-free 0.258
1U31 recombinant human heart transhydrogenase dIII bound with NADPH Deposited 2004-07-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 880–1086（207 aa）	Not recorded	SO4 SULFATE ION × 1 NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；281 K；ammonium sulphate, MES, dioxane, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 281K	Resolution 2.20 Å R-free 0.268
1U31 recombinant human heart transhydrogenase dIII bound with NADPH Deposited 2004-07-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 880–1086（207 aa）	Not recorded	SO4 SULFATE ION × 1 NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；281 K；ammonium sulphate, MES, dioxane, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 281K	Resolution 2.20 Å R-free 0.268
1U31 recombinant human heart transhydrogenase dIII bound with NADPH Deposited 2004-07-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 880–1086（207 aa） Chain B 880–1086（207 aa）	Not recorded	SO4 SULFATE ION × 2 NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；281 K；ammonium sulphate, MES, dioxane, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 281K	Resolution 2.20 Å R-free 0.268
1U31 recombinant human heart transhydrogenase dIII bound with NADPH Deposited 2004-07-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 880–1086（207 aa）	Not recorded	SO4 SULFATE ION × 2 NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；281 K；ammonium sulphate, MES, dioxane, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 281K	Resolution 2.20 Å R-free 0.268
1U31 recombinant human heart transhydrogenase dIII bound with NADPH Deposited 2004-07-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 880–1086（207 aa）	Not recorded	SO4 SULFATE ION × 2 NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；281 K；ammonium sulphate, MES, dioxane, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 281K	Resolution 2.20 Å R-free 0.268

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

View Construct and Data Evidence

UniProt name	NNTM_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–207； UniProt 880–1086 Author chain B； PDBConstruct 1–207； UniProt 880–1086

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	1pt9
Deposition date deposition_date	2003-06-23
Structure title title	Crystal Structure Analysis of the DIII Component of Transhydrogenase with a Thio-Nicotinamide Nucleotide Analogue
Keywords keywords	Transhydrogenase, thio-nicotinamide, mitochondria, proton translocation, OXIDOREDUCTASE; OXIDOREDUCTASE
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	25.32 Å
Radius of gyration Rg (electron density) rg_electron	24.54 Å
Forward intensity I(0) i0	30128900.00
Molecular weight molecular_weight	41227.0 kDa
Excluded volume excluded_volume	51241 Å³
Envelope volume envelope_volume	63379 Å³
Hydration-shell volume shell_volume	21938 Å³
Envelope diameter envelope_diameter	83.7 Å
Shell Rg shell_rg	31.03 Å
Envelope Rg envelope_rg	24.63 Å
Shape Rg shape_rg	24.50 Å
Total Rg total_rg	25.40 Å
Total atoms total_atoms	2872
Residues n_residues	364
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	81.7 Å
Rg (real space) rg_real	25.38 Å
Rg uncertainty (real space) rg_real_error	0.55 Å
I(0) (real space) i0_real	3.0130e+07
I(0) uncertainty (real space) i0_real_error	4.1940e+05
Rg (reciprocal space) rg_reciprocal	25.37 Å
I(0) (reciprocal space) i0_reciprocal	30130000.0000
Solution quality estimate total_estimate	0.8683
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.3 Å
Skewness Skewness skewness	0.341
Kurtosis Kurtosis kurtosis	-0.640
Angular range angular_range	— – 0.3150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8644000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.817; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.883; Smooth: 0.950

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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(P) transhydrogenase, mitochondrial
Molecular weight formula_weight	22281.7 kDa
EC 编号 ec_number	1.6.1.2
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3043

MNRSLANVILGGYGTTSTAGGKPMEISGTHTEINLDNAIDMIREANSIIITPGYGLCAAKAQYPIADLVKMLTEQGKKVRFGIHPVAGRMPGQLNVLLAEAGVPYDIVLEMDEINHDFPDTDLVLVIGANDTVNSAAQEDPNSIIAGMPVLEVWKSKQVIVMKRSLGVGYAAVDNPIFYKPNTAMLLGDAKKTCDALQAKVRESYQK

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	7-THIONICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Molecular weight formula_weight	759.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	171

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1pt9a_
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.31.1.4 — Transhydrogenase domain III (dIII)

Domain ID domain_id	d1pt9b_
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.31.1.4 — Transhydrogenase domain III (dIII)

CATH v4.4 (2 domains)

Domain ID domain_id	1pt9A00
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	1pt9B00
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

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8. Citations (1)

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Unit-cell length a length_a	57.400 Å
Unit-cell length b length_b	57.400 Å
Unit-cell length c length_c	251.130 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	16

Space group space_group	P 41 2 2
Space-group number int_tables_number	91
Crystal system crystal_system	—

Resolution resolution	2.420 Å
Low-resolution limit resolution_low	36.800 Å
R factor r_factor	—
R_work r_work	0.2190
R_free r_free	0.2780

fit	/app/data/saxs_computation/pt/1pt9/1pt9.fit
pddf	/app/data/pr_computation/pt/1pt9/1pt9.pr.out
profile	/app/data/saxs_computation/pt/1pt9/1pt9.dat

Crystal Structure Analysis of the DIII Component of Transhydrogenase with a Thio-Nicotinamide Nucleotide Analogue

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

NAD(P) transhydrogenase, mitochondrial

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