SAXSdb — 1flk

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

TNF RECEPTOR ASSOCIATED FACTOR 3

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 homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 341–568	Fragment：TRAF DOMAIN	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；METHANOL, SODIUM CHLORIDE, TRIS BUFFER, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.80 Å R-free 0.286
2	Protein homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain B； UniProt 341–568	Fragment：TRAF DOMAIN	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；METHANOL, SODIUM CHLORIDE, TRIS BUFFER, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.80 Å R-free 0.286

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 1FLK	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1FLL MOLECULAR BASIS FOR CD40 SIGNALING MEDIATED BY TRAF3 Deposited 2000-08-14	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 341–568（228 aa） Fragment：TRAF DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；METHANOL, SODIUM CHLORIDE, TRIS BUFFER, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 3.50 Å R-free 0.312
1FLL MOLECULAR BASIS FOR CD40 SIGNALING MEDIATED BY TRAF3 Deposited 2000-08-14	Different oligomeric state Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 341–568（228 aa） Fragment：TRAF DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；METHANOL, SODIUM CHLORIDE, TRIS BUFFER, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 3.50 Å R-free 0.312
1FLL MOLECULAR BASIS FOR CD40 SIGNALING MEDIATED BY TRAF3 Deposited 2000-08-14	Different oligomeric state Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 341–568（228 aa） Fragment：TRAF DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；METHANOL, SODIUM CHLORIDE, TRIS BUFFER, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 3.50 Å R-free 0.312
1KZZ DOWNSTREAM REGULATOR TANK BINDS TO THE CD40 RECOGNITION SITE ON TRAF3 Deposited 2002-02-08	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 377–568（192 aa） Fragment：Residues 377-568	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.7；298 K；100mM MES, 15% PEG1000, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 3.50 Å R-free 0.307
1KZZ DOWNSTREAM REGULATOR TANK BINDS TO THE CD40 RECOGNITION SITE ON TRAF3 Deposited 2002-02-08	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 377–568（192 aa） Fragment：Residues 377-568	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.7；298 K；100mM MES, 15% PEG1000, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 3.50 Å R-free 0.307
1L0A DOWNSTREAM REGULATOR TANK BINDS TO THE CD40 RECOGNITION SITE ON TRAF3 Deposited 2002-02-08	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 377–568（192 aa） Fragment：Residues 377-568	Mutation：T195K	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；298 K；100mM MES, 15% PEG1000, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.90 Å R-free 0.295
1L0A DOWNSTREAM REGULATOR TANK BINDS TO THE CD40 RECOGNITION SITE ON TRAF3 Deposited 2002-02-08	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 377–568（192 aa） Fragment：Residues 377-568	Mutation：T195K	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；298 K；100mM MES, 15% PEG1000, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.90 Å R-free 0.295
1RF3 Structurally Distinct Recognition Motifs in Lymphotoxin-B Receptor and CD40 for TRAF-mediated Signaling Deposited 2003-11-07	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 377–568（192 aa） Fragment：Recognition motif (residues 377-568)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；15% PEG4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 3.50 Å R-free 0.315
1ZMS LMP1 Protein binds to TRAF3 as a structural CD40 Deposited 2005-05-10	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 377–568（192 aa） Fragment：Sequence database residues 377-568	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；15% PEG 4000, 0.1 M MES, pH 6.5, temperature 298K, VAPOR DIFFUSION, HANGING DROP	Resolution 2.80 Å R-free 0.255
1ZMS LMP1 Protein binds to TRAF3 as a structural CD40 Deposited 2005-05-10	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 377–568（192 aa） Fragment：Sequence database residues 377-568	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；15% PEG 4000, 0.1 M MES, pH 6.5, temperature 298K, VAPOR DIFFUSION, HANGING DROP	Resolution 2.80 Å R-free 0.255
2ECY Solution structure of the Zinc finger, C3HC4 type (RING finger)" domain of TNF receptor-associated factor 3 Deposited 2007-02-14	Different construct 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 43–101（59 aa） Fragment：RING-type, residues 8-66	Not recorded	ZN ZINC ION × 2	SOLUTION NMR NMR measurement conditions pH 7；296 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR sample composition 1.10mM Protein; 20mM d-Tris-HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 50uM Zncl2+1mM IDA; 10% D2O, 90% H2O \| 90% H2O/10% D2O	Resolution not provided
2GKW Key contacts promote recongnito of BAFF-R by TRAF3 Deposited 2006-04-03	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 377–568（192 aa） Fragment：TRAF domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；15% PEG 4000, 0.1 M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.70 Å R-free 0.260
8T5P SARS-CoV-2 ORF3a peptide in complex with TRAF3 TRAF domain Deposited 2023-06-14	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 377–568（192 aa） Fragment：TRAF domain (UNP residues 377-568) Chain B 377–568（192 aa） Fragment：TRAF domain (UNP residues 377-568) Chain C 377–568（192 aa） Fragment：TRAF domain (UNP residues 377-568)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293.15 K；13% PEG3350, 0.1 M Tris, pH 8.0, 0.25 M ammonium sulfate	Resolution 2.50 Å R-free 0.242
8T5P SARS-CoV-2 ORF3a peptide in complex with TRAF3 TRAF domain Deposited 2023-06-14	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 377–568（192 aa） Fragment：TRAF domain (UNP residues 377-568) Chain E 377–568（192 aa） Fragment：TRAF domain (UNP residues 377-568) Chain F 377–568（192 aa） Fragment：TRAF domain (UNP residues 377-568)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293.15 K；13% PEG3350, 0.1 M Tris, pH 8.0, 0.25 M ammonium sulfate	Resolution 2.50 Å R-free 0.242
8ZUK Cluster structure of the BAFF-BAFFR-TRAF3 complex Deposited 2024-06-09	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 42 PDB declaration: 42-meric	Chain A 267–568（302 aa） Chain B 267–568（302 aa） Chain C 267–568（302 aa） Chain G 267–568（302 aa） Chain H 267–568（302 aa） Chain I 267–568（302 aa） Chain M 267–568（302 aa） Chain N 267–568（302 aa） Chain O 267–568（302 aa） Chain S 267–568（302 aa） Chain T 267–568（302 aa） Chain U 267–568（302 aa） Chain Y 267–568（302 aa） Chain Z 267–568（302 aa） Chain a 267–568（302 aa） Chain e 267–568（302 aa） Chain f 267–568（302 aa） Chain g 267–568（302 aa） Chain k 267–568（302 aa） Chain l 267–568（302 aa） Chain m 267–568（302 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.83 Å

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

View Construct and Data Evidence

UniProt name	TRAF3_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–228； UniProt 341–568 Author chain B； PDBConstruct 1–228； UniProt 341–568

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	1flk
Deposition date deposition_date	2000-08-14
Structure title title	MOLECULAR BASIS FOR CD40 SIGNALING MEDIATED BY TRAF3
Keywords keywords	TNF SIGNALING, TRAF3, CD40-BINDING PROTEIN, APOPTOSIS; APOPTOSIS
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	— Å
Radius of gyration Rg (electron density) rg_electron	128.00 Å
Forward intensity I(0) i0	28717500.00
Molecular weight molecular_weight	46299.0 kDa
Excluded volume excluded_volume	58153 Å³
Envelope volume envelope_volume	219680 Å³
Hydration-shell volume shell_volume	15505 Å³
Envelope diameter envelope_diameter	305.9 Å
Shell Rg shell_rg	126.00 Å
Envelope Rg envelope_rg	104.80 Å
Shape Rg shape_rg	128.00 Å
Total Rg total_rg	127.70 Å
Total atoms total_atoms	3252
Residues n_residues	410
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	319.4 Å
Rg (real space) rg_real	127.20 Å
Rg uncertainty (real space) rg_real_error	4.58 Å
I(0) (real space) i0_real	2.8720e+07
I(0) uncertainty (real space) i0_real_error	8.2360e+05
Rg (reciprocal space) rg_reciprocal	86.39 Å
I(0) (reciprocal space) i0_reciprocal	25290000.0000
Solution quality estimate total_estimate	0.3078
Solution quality rating solution_quality	SUSPICIOUS a SUSPICIOUS solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	26.6 Å
Skewness Skewness skewness	0.051
Kurtosis Kurtosis kurtosis	-1.888
Angular range angular_range	— – 0.0600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	9329000.0000
Real-space data points n_real_points	13
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.000; Stabil: 1.000; Sysdev: 0.000; Positv: 0.998; Valcen: 0.000; Smooth: 0.000

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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) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1flka1
Class class	b — All beta proteins
Fold Fold fold	b.8 — TRAF domain-like
Superfamily Superfamily superfamily	b.8.1 — TRAF domain-like
Family Family family	b.8.1.1 — MATH domain

Domain ID domain_id	d1flka2
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.2 — Trimerization domain of TRAF
Family Family family	h.1.2.1 — Trimerization domain of TRAF

Domain ID domain_id	d1flkb1
Class class	b — All beta proteins
Fold Fold fold	b.8 — TRAF domain-like
Superfamily Superfamily superfamily	b.8.1 — TRAF domain-like
Family Family family	b.8.1.1 — MATH domain

Domain ID domain_id	d1flkb2
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.2 — Trimerization domain of TRAF
Family Family family	h.1.2.1 — Trimerization domain of TRAF

CATH v4.4 (2 domains)

Domain ID domain_id	1flkA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	210 — Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A
Homologous superfamily homologous superfamily	10 — Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A

Domain ID domain_id	1flkB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	210 — Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A
Homologous superfamily homologous superfamily	10 — Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A

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8. Citations (1)

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Unit-cell length a length_a	84.530 Å
Unit-cell length b length_b	84.530 Å
Unit-cell length c length_c	319.500 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	18

Space group space_group	H 3
Space-group number int_tables_number	146
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.2240
R_work r_work	0.2240
R_free r_free	0.2860

Description description	TNF RECEPTOR ASSOCIATED FACTOR 3
Molecular weight formula_weight	25885.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3252

MOLECULAR BASIS FOR CD40 SIGNALING MEDIATED BY TRAF3

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

TNF RECEPTOR ASSOCIATED FACTOR 3

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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

fit	/app/data/saxs_computation/fl/1flk/1flk.fit
pddf	/app/data/pr_computation/fl/1flk/1flk.pr.out
profile	/app/data/saxs_computation/fl/1flk/1flk.dat