SAXSdb — 2kn1

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

Tumor necrosis factor receptor superfamily member 17

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 2–50	Fragment：residues 2-50 Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 6；Ionic strength (raw mmCIF value) 10；Pressure ambient NMR sample composition：900 uM BCMA, 10 mM sodium phosphate, 0.02 % sodium azide, 95% H2O, 5% D2O \| 95% H2O/5% 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 2KN1	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1OQD Crystal structure of sTALL-1 and BCMA Deposited 2003-03-07	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 108 PDB declaration: 108-meric	Chain K 8–46（39 aa） Fragment：extracellular domain Chain L 8–46（39 aa） Fragment：extracellular domain Chain M 8–46（39 aa） Fragment：extracellular domain Chain N 8–46（39 aa） Fragment：extracellular domain Chain O 8–46（39 aa） Fragment：extracellular domain Chain P 8–46（39 aa） Fragment：extracellular domain Chain Q 8–46（39 aa） Fragment：extracellular domain Chain R 8–46（39 aa） Fragment：extracellular domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；277 K；dioxane, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.60 Å R-free 0.260
1XU2 The crystal structure of APRIL bound to BCMA Deposited 2004-10-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain R 5–51（47 aa） Fragment：BCMA ECD Chain S 5–51（47 aa） Fragment：BCMA ECD Chain T 5–51（47 aa） Fragment：BCMA ECD	Not recorded	NI NICKEL (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；292 K；well solution: 0.1M MES, 5% Peg 8000, 10% Peg 1000, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K	Resolution 2.35 Å R-free 0.213
4ZFO J22.9-xi: chimeric mouse/human antibody against human BCMA (CD269) Deposited 2015-04-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 1–54（54 aa） Fragment：Extracellular (N-terminal) domain, UNP residues 1-54	Not recorded	CU COPPER (II) ION × 1 BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293.15 K；1 microliter of the complex at 8 mg/ml with 2 microliters of 21% PEG 3350, 0.1 M BisTris pH 6.5 and 5 mM CuCl2	Resolution 1.90 Å R-free 0.209
4ZFO J22.9-xi: chimeric mouse/human antibody against human BCMA (CD269) Deposited 2015-04-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain K 1–54（54 aa） Fragment：Extracellular (N-terminal) domain, UNP residues 1-54	Not recorded	CU COPPER (II) ION × 2 BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293.15 K；1 microliter of the complex at 8 mg/ml with 2 microliters of 21% PEG 3350, 0.1 M BisTris pH 6.5 and 5 mM CuCl2	Resolution 1.90 Å R-free 0.209
6J7W Crystal Structure of Human BCMA in complex with UniAb(TM) VH Deposited 2019-01-18	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 6–44（39 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4；293 K；0.2M sodium malonate pH 4.0 and 20% PEG 3350	Resolution 2.60 Å R-free 0.271
6J7W Crystal Structure of Human BCMA in complex with UniAb(TM) VH Deposited 2019-01-18	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 6–44（39 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4；293 K；0.2M sodium malonate pH 4.0 and 20% PEG 3350	Resolution 2.60 Å R-free 0.271
8HXQ Nanobody1 in complex with human BCMA ECD Deposited 2023-01-05	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–54（54 aa） Chain D 1–54（54 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.1；293 K；0.2 M Ammonium sulfate, 20% w/v Polyethylene glycol 3350, pH6.1	Resolution 2.40 Å R-free 0.274
8HXR Nanobody2 in complex with human BCMA ECD Deposited 2023-01-05	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–54（54 aa） Chain D 1–54（54 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；1.8 M Sodium acetate trihydrate, 0.1 M Bis-Tris Propane pH7.0	Resolution 2.70 Å R-free 0.287
8QY9 J22.9-H, fully humanized Fab Fragment based on chimeric J22.9-xi IgG against BCMA Deposited 2023-10-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 7–41（35 aa）	Not recorded	CU COPPER (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293.15 K；14% PEG 3350 100 mM BisTris 7.5 mM Cu(II)	Resolution 3.10 Å R-free 0.301
8QYA J22.9-FNY, fully humanized, CDR optimized Fab Fragment based on chimeric J22.9-xi IgG against BCMA; with VH CDR2 glycosylation Deposited 2023-10-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 6–41（36 aa）	Not recorded	CU COPPER (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；PEG 3350 CuCl2 BisTris	Resolution 2.72 Å R-free 0.299
8QYB J22.9-ISY, fully humanized and CDR optimized Fab Fragment based on chimeric J22.9-xi IgG against BCMA Deposited 2023-10-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 7–41（35 aa）	Not recorded	CU COPPER (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；14% PEG 3350 7.5 mM CuCl2 BisTris	Resolution 3.09 Å R-free 0.288
9MQO Crystal structure of BCMA in complex with CA10v2 Fab Deposited 2025-01-04	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: 18-meric	Chain A 1–54（54 aa） Chain D 1–54（54 aa） Chain G 1–54（54 aa） Chain J 1–54（54 aa） Chain M 1–54（54 aa） Chain P 1–54（54 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.18 M Sodium Chloride, 0.09 M Phosphate/citrate pH 4.2, 20 % w/v PEG 8000, 0.1M Sodium Malonate	Resolution 3.18 Å R-free 0.272

10 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TNR17_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–49； UniProt 2–50

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	2kn1
Deposition date deposition_date	2009-08-11
Structure title title	Solution NMR Structure of BCMA
Keywords keywords	BCMA, BAFF, TNF Receptor, CRD, APRIL, SIGNALING PROTEIN; SIGNALING PROTEIN
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	11.74 Å
Radius of gyration Rg (electron density) rg_electron	12.02 Å
Forward intensity I(0) i0	221314000.00
Molecular weight molecular_weight	112010.0 kDa
Excluded volume excluded_volume	135210 Å³
Envelope volume envelope_volume	25231 Å³
Hydration-shell volume shell_volume	13381 Å³
Envelope diameter envelope_diameter	55.4 Å
Shell Rg shell_rg	21.99 Å
Envelope Rg envelope_rg	17.15 Å
Shape Rg shape_rg	11.98 Å
Total Rg total_rg	12.49 Å
Total atoms total_atoms	15080
Residues n_residues	980
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	50.6 Å
Rg (real space) rg_real	11.90 Å
Rg uncertainty (real space) rg_real_error	0.62 Å
I(0) (real space) i0_real	2.2130e+08
I(0) uncertainty (real space) i0_real_error	2.8160e+06
Rg (reciprocal space) rg_reciprocal	11.89 Å
I(0) (reciprocal space) i0_reciprocal	221300000.0000
Solution quality estimate total_estimate	0.6997
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	12.2 Å
Skewness Skewness skewness	0.690
Kurtosis Kurtosis kurtosis	0.415
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	91930.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.317; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.146; 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	2kn1A00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	1290 — Tumor necrosis factor receptor fold
Homologous superfamily homologous superfamily	10 — Tumor necrosis factor receptor superfamily

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8. Citations (1)

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Description description	Tumor necrosis factor receptor superfamily member 17
Molecular weight formula_weight	5601.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	15080

fit	/app/data/saxs_computation/kn/2kn1/2kn1.fit
pddf	/app/data/pr_computation/kn/2kn1/2kn1.pr.out
profile	/app/data/saxs_computation/kn/2kn1/2kn1.dat

Solution NMR Structure of BCMA

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

Tumor necrosis factor receptor superfamily member 17

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

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)