SAXSdb — 1wwy

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

Thioredoxin-like protein 1

Homo sapiens

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 122–279	Fragment：DUF1000 domain	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 7；298 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR sample composition：1.02mM DUF1000 domain, 20mM Tris-HCl, 100mM NaCl, 1mM d-DTT, 0.02% NaN3 \| 90% H2O/10% D2O	Resolution not provided

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 1WWY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1GH2 Crystal structure of the catalytic domain of a new human thioredoxin-like protein Deposited 2000-11-01	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–108（107 aa） Fragment：RESIDUES 2 - 108, CATALYTIC N-TERMINAL DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 5；291 K；ammonium sulfate, pH 5.0, EVAPORATION, temperature 291.0K	Resolution 2.22 Å R-free 0.253
9BW4 TXNL1-bound proteasome Deposited 2024-05-20	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 40 PDB declaration: 40-meric	Chain x 1–289（289 aa）	Not recorded	ZN ZINC ION × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 3 MG MAGNESIUM ION × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
9E8G Nub1/Fat10-processing human 26S proteasome bound to Txnl1 with Rpt5 at top of spiral staircase Deposited 2024-11-05	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric	Chain u 1–289（289 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 3 MG MAGNESIUM ION × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 3 ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；30 mM HEPES pH7.4, 25 mM NaCl, 25 mM KCl, 3% (v/v) glycerol, 5 mM MgCl2 2 mM ATP and 0.5 mM TCEP. cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.01 Å
9E8H Human proteasome in resting state conformation bound to TXNL1 in backward conformation Deposited 2024-11-05	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 27 PDB declaration: 27-meric	Chain u 1–289（289 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 5 MG MAGNESIUM ION × 6 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；30 mM HEPES pH7.4, 25 mM NaCl, 25 mM KCl, 3% (v/v) glycerol, 5 mM MgCl2 2 mM ATP and 0.5 mM TCEP. cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
9E8I Human proteasome in resting state conformation bound to TXNL1 in Forward conformation Deposited 2024-11-05	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 27 PDB declaration: 27-meric	Chain u 1–289（289 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 5 MG MAGNESIUM ION × 6 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；30 mM HEPES pH7.4, 25 mM NaCl, 25 mM KCl, 3% (v/v) glycerol, 5 mM MgCl2 2 mM ATP and 0.5 mM TCEP. cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.87 Å
9E8J Nub1/Fat10-processing human 26S proteasome bound to Txnl1 with Rpt1 at top of spiral staircase Deposited 2024-11-05	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 28 PDB declaration: 28-meric	Chain u 1–289（289 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；30 mM HEPES pH7.4, 25 mM NaCl, 25 mM KCl, 3% (v/v) glycerol, 5 mM MgCl2 2 mM ATP and 0.5 mM TCEP. cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.47 Å
9E8L Nub1/Fat10-processing human 26S proteasome bound to Txnl1 with Rpt4 at top of spiral staircase Deposited 2024-11-05	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 28 PDB declaration: 28-meric	Chain u 1–289（289 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 4 MG MAGNESIUM ION × 3 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；30 mM HEPES pH7.4, 25 mM NaCl, 25 mM KCl, 3% (v/v) glycerol, 5 mM MgCl2 2 mM ATP and 0.5 mM TCEP. cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.59 Å
9E8O Nub1/Fat10-processing human 26S proteasome bound to Txnl1 with Rpt2 at top of spiral staircase and partially unfolded Eos Deposited 2024-11-05	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 34 PDB declaration: 34-meric	Chain u 1–289（289 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 4 ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；30 mM HEPES pH7.4, 25 mM NaCl, 25 mM KCl, 3% (v/v) glycerol, 5 mM MgCl2 2 mM ATP and 0.5 mM TCEP cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å

8 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TXNL1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 8–165； UniProt 122–279

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	1wwy
Deposition date deposition_date	2005-01-18
Structure title title	Solution structure of the DUF1000 domain of a thioredoxin-like protein 1
Keywords keywords	;structural genomics, hypothetical protein, regulatory protein, apoptosis, cancer, RIKEN Structural Genomics/Proteomics Initiative, RSGI ;; APOPTOSIS
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	17.18 Å
Radius of gyration Rg (electron density) rg_electron	16.36 Å
Forward intensity I(0) i0	2155610000.00
Molecular weight molecular_weight	380760.0 kDa
Excluded volume excluded_volume	469760 Å³
Envelope volume envelope_volume	51611 Å³
Hydration-shell volume shell_volume	20648 Å³
Envelope diameter envelope_diameter	72.8 Å
Shell Rg shell_rg	27.99 Å
Envelope Rg envelope_rg	23.28 Å
Shape Rg shape_rg	16.35 Å
Total Rg total_rg	16.55 Å
Total atoms total_atoms	52040
Residues n_residues	3420
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	68.1 Å
Rg (real space) rg_real	17.22 Å
Rg uncertainty (real space) rg_real_error	0.67 Å
I(0) (real space) i0_real	2.1560e+09
I(0) uncertainty (real space) i0_real_error	3.4220e+07
Rg (reciprocal space) rg_reciprocal	17.21 Å
I(0) (reciprocal space) i0_reciprocal	2156000000.0000
Solution quality estimate total_estimate	0.7591
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.5 Å
Skewness Skewness skewness	0.519
Kurtosis Kurtosis kurtosis	0.321
Angular range angular_range	— – 0.4650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1397000.0000
Real-space data points n_real_points	77
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.369; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.761; Smooth: 0.996

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	1wwyA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	470 — PITH domain

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8. Citations (1)

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Description description	Thioredoxin-like protein 1
Molecular weight formula_weight	19083.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	52040

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606

fit	/app/data/saxs_computation/ww/1wwy/1wwy.fit
pddf	/app/data/pr_computation/ww/1wwy/1wwy.pr.out
profile	/app/data/saxs_computation/ww/1wwy/1wwy.dat

Solution structure of the DUF1000 domain of a thioredoxin-like protein 1

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

Thioredoxin-like protein 1

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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)