6fxn

Crystal structure of human BAFF in complex with Fab fragment of anti-BAFF antibody belimumab

Method: X-RAY DIFFRACTION D_max: 213.2 Å Quality: GOOD

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

Tumor necrosis factor ligand superfamily member 13B

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 heterocomplex Heteromer Protein × 9 PDB declaration: nonameric（9） Consistent with protein copy count	Chain A； UniProt 134–285 Chain B； UniProt 134–285 Chain C； UniProt 134–285	Mutation：H218A	belimumab heavy chain × 3 belimumab light chain × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；293 K；9% (w/v) PEG4000, 0.1 M MgCl2, 0.1 M HEPES pH 7.5	Resolution 2.90 Å R-free 0.231
2	Protein heterocomplex Heteromer Protein × 9 PDB declaration: nonameric（9） Consistent with protein copy count	Chain J； UniProt 134–285 Chain K； UniProt 134–285 Chain L； UniProt 134–285	Mutation：H218A	belimumab heavy chain × 3 belimumab light chain × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；293 K；9% (w/v) PEG4000, 0.1 M MgCl2, 0.1 M HEPES pH 7.5	Resolution 2.90 Å R-free 0.231

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 6FXN	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1JH5 Crystal Structure of sTALL-1 of TNF family ligand Deposited 2001-06-27	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 60 PDB declaration: 60-meric	Chain A 142–285（144 aa） Fragment：sTALL-1, soluble part of TALL-1 Chain B 142–285（144 aa） Fragment：sTALL-1, soluble part of TALL-1 Chain C 142–285（144 aa） Fragment：sTALL-1, soluble part of TALL-1 Chain D 142–285（144 aa） Fragment：sTALL-1, soluble part of TALL-1 Chain E 142–285（144 aa） Fragment：sTALL-1, soluble part of TALL-1 Chain F 142–285（144 aa） Fragment：sTALL-1, soluble part of TALL-1 Chain G 142–285（144 aa） Fragment：sTALL-1, soluble part of TALL-1 Chain H 142–285（144 aa） Fragment：sTALL-1, soluble part of TALL-1 Chain I 142–285（144 aa） Fragment：sTALL-1, soluble part of TALL-1 Chain J 142–285（144 aa） Fragment：sTALL-1, soluble part of TALL-1	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；277 K；35% dioxane, pH 9.0, VAPOR DIFFUSION, HANGING DROP at 277K	Resolution 3.00 Å R-free 0.252
1KD7 Crystal structure of an extracellular domain fragment of human BAFF Deposited 2001-11-12	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 122–285（164 aa） Fragment：Extracellular domain fragment Chain B 122–285（164 aa） Fragment：Extracellular domain fragment Chain C 122–285（164 aa） Fragment：Extracellular domain fragment	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；277 K；8% PEG 4000, 0.1 M sodium acetatesolution of 8% PEG 4000, 0.1 M sodium acetate pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.80 Å R-free 0.250
1KD7 Crystal structure of an extracellular domain fragment of human BAFF Deposited 2001-11-12	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain K 122–285（164 aa） Fragment：Extracellular domain fragment Chain L 122–285（164 aa） Fragment：Extracellular domain fragment Chain M 122–285（164 aa） Fragment：Extracellular domain fragment	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；277 K；8% PEG 4000, 0.1 M sodium acetatesolution of 8% PEG 4000, 0.1 M sodium acetate pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.80 Å R-free 0.250
1KXG The 2.0 Ang Resolution Structure of BLyS, B Lymphocyte Stimulator. Deposited 2002-01-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 134–285（152 aa） Fragment：soluble portion (residues 134-285) Chain B 134–285（152 aa） Fragment：soluble portion (residues 134-285) Chain C 134–285（152 aa） Fragment：soluble portion (residues 134-285)	Not recorded	MG MAGNESIUM ION × 4 CIT CITRIC ACID × 1 DIO 1,4-DIETHYLENE DIOXIDE × 13	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；279 K；25% dioxane, 25 mM MgCl2, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 279.0K	Resolution 2.00 Å R-free 0.209
1KXG The 2.0 Ang Resolution Structure of BLyS, B Lymphocyte Stimulator. Deposited 2002-01-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain D 134–285（152 aa） Fragment：soluble portion (residues 134-285) Chain E 134–285（152 aa） Fragment：soluble portion (residues 134-285) Chain F 134–285（152 aa） Fragment：soluble portion (residues 134-285)	Not recorded	MG MAGNESIUM ION × 3 CIT CITRIC ACID × 1 DIO 1,4-DIETHYLENE DIOXIDE × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；279 K；25% dioxane, 25 mM MgCl2, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 279.0K	Resolution 2.00 Å R-free 0.209
1OQD Crystal structure of sTALL-1 and BCMA Deposited 2003-03-07	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 108 PDB declaration: 108-meric	Chain A 142–285（144 aa） Fragment：extracellular domain Chain B 142–285（144 aa） Fragment：extracellular domain Chain C 142–285（144 aa） Fragment：extracellular domain Chain D 142–285（144 aa） Fragment：extracellular domain Chain E 142–285（144 aa） Fragment：extracellular domain Chain F 142–285（144 aa） Fragment：extracellular domain Chain G 142–285（144 aa） Fragment：extracellular domain Chain H 142–285（144 aa） Fragment：extracellular domain Chain I 142–285（144 aa） Fragment：extracellular domain Chain J 142–285（144 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
1OQE Crystal structure of sTALL-1 with BAFF-R Deposited 2003-03-07	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 108 PDB declaration: 108-meric	Chain A 142–285（144 aa） Fragment：extracellular domain Chain B 142–285（144 aa） Fragment：extracellular domain Chain C 142–285（144 aa） Fragment：extracellular domain Chain D 142–285（144 aa） Fragment：extracellular domain Chain E 142–285（144 aa） Fragment：extracellular domain Chain F 142–285（144 aa） Fragment：extracellular domain Chain G 142–285（144 aa） Fragment：extracellular domain Chain H 142–285（144 aa） Fragment：extracellular domain Chain I 142–285（144 aa） Fragment：extracellular domain Chain J 142–285（144 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；dioxane, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 100K	Resolution 2.50 Å R-free 0.259
1OSG Complex between BAFF and a BR3 derived peptide presented in a beta-hairpin scaffold Deposited 2003-03-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 82–285（204 aa） Fragment：TNF domain Chain B 82–285（204 aa） Fragment：TNF domain Chain C 82–285（204 aa） Fragment：TNF domain	Not recorded	MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.7；292 K；20% PEG 3350, 1.0 M LiCl, 0.1M sodium cacodylate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 3.00 Å R-free 0.286
1OSG Complex between BAFF and a BR3 derived peptide presented in a beta-hairpin scaffold Deposited 2003-03-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain D 82–285（204 aa） Fragment：TNF domain Chain E 82–285（204 aa） Fragment：TNF domain Chain F 82–285（204 aa） Fragment：TNF domain	Not recorded	MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.7；292 K；20% PEG 3350, 1.0 M LiCl, 0.1M sodium cacodylate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 3.00 Å R-free 0.286
3V56 Re-refinement of PDB entry 1OSG - Complex between BAFF and a BR3 derived peptide presented in a beta-hairpin scaffold - reveals an additonal copy of the peptide. Deposited 2011-12-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 82–285（204 aa） Chain B 82–285（204 aa） Chain C 82–285（204 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.00 Å R-free 0.200
3V56 Re-refinement of PDB entry 1OSG - Complex between BAFF and a BR3 derived peptide presented in a beta-hairpin scaffold - reveals an additonal copy of the peptide. Deposited 2011-12-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain D 82–285（204 aa） Chain E 82–285（204 aa） Chain F 82–285（204 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.00 Å R-free 0.200
4V46 Crystal structure of the BAFF-BAFF-R complex Deposited 2003-03-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 120 PDB declaration: 120-meric	Chain A0 138–285（148 aa） Fragment：residues 138-285 Chain A1 138–285（148 aa） Fragment：residues 138-285 Chain A2 138–285（148 aa） Fragment：residues 138-285 Chain A3 138–285（148 aa） Fragment：residues 138-285 Chain A4 138–285（148 aa） Fragment：residues 138-285 Chain A5 138–285（148 aa） Fragment：residues 138-285 Chain A6 138–285（148 aa） Fragment：residues 138-285 Chain A7 138–285（148 aa） Fragment：residues 138-285 Chain A8 138–285（148 aa） Fragment：residues 138-285 Chain A9 138–285（148 aa） Fragment：residues 138-285 Chain AA 138–285（148 aa） Fragment：residues 138-285 Chain AB 138–285（148 aa） Fragment：residues 138-285 Chain AC 138–285（148 aa） Fragment：residues 138-285 Chain AD 138–285（148 aa） Fragment：residues 138-285 Chain AE 138–285（148 aa） Fragment：residues 138-285 Chain AF 138–285（148 aa） Fragment：residues 138-285 Chain AG 138–285（148 aa） Fragment：residues 138-285 Chain AH 138–285（148 aa） Fragment：residues 138-285 Chain AI 138–285（148 aa） Fragment：residues 138-285 Chain AJ 138–285（148 aa） Fragment：residues 138-285 Chain AK 138–285（148 aa） Fragment：residues 138-285 Chain AL 138–285（148 aa） Fragment：residues 138-285 Chain AM 138–285（148 aa） Fragment：residues 138-285 Chain AN 138–285（148 aa） Fragment：residues 138-285 Chain AO 138–285（148 aa） Fragment：residues 138-285 Chain AP 138–285（148 aa） Fragment：residues 138-285 Chain AQ 138–285（148 aa） Fragment：residues 138-285 Chain AR 138–285（148 aa） Fragment：residues 138-285 Chain AS 138–285（148 aa） Fragment：residues 138-285 Chain AT 138–285（148 aa） Fragment：residues 138-285 Chain AU 138–285（148 aa） Fragment：residues 138-285 Chain AV 138–285（148 aa） Fragment：residues 138-285 Chain AW 138–285（148 aa） Fragment：residues 138-285 Chain AX 138–285（148 aa） Fragment：residues 138-285 Chain AY 138–285（148 aa） Fragment：residues 138-285 Chain AZ 138–285（148 aa） Fragment：residues 138-285 Chain Aa 138–285（148 aa） Fragment：residues 138-285 Chain Ab 138–285（148 aa） Fragment：residues 138-285 Chain Ac 138–285（148 aa） Fragment：residues 138-285 Chain Ad 138–285（148 aa） Fragment：residues 138-285 Chain Ae 138–285（148 aa） Fragment：residues 138-285 Chain Af 138–285（148 aa） Fragment：residues 138-285 Chain Ag 138–285（148 aa） Fragment：residues 138-285 Chain Ah 138–285（148 aa） Fragment：residues 138-285 Chain Ai 138–285（148 aa） Fragment：residues 138-285 Chain Aj 138–285（148 aa） Fragment：residues 138-285 Chain Ak 138–285（148 aa） Fragment：residues 138-285 Chain Al 138–285（148 aa） Fragment：residues 138-285 Chain Am 138–285（148 aa） Fragment：residues 138-285 Chain An 138–285（148 aa） Fragment：residues 138-285 Chain Ao 138–285（148 aa） Fragment：residues 138-285 Chain Ap 138–285（148 aa） Fragment：residues 138-285 Chain Aq 138–285（148 aa） Fragment：residues 138-285 Chain Ar 138–285（148 aa） Fragment：residues 138-285 Chain As 138–285（148 aa） Fragment：residues 138-285 Chain At 138–285（148 aa） Fragment：residues 138-285 Chain Au 138–285（148 aa） Fragment：residues 138-285 Chain Av 138–285（148 aa） Fragment：residues 138-285 Chain Aw 138–285（148 aa） Fragment：residues 138-285 Chain Ax 138–285（148 aa） Fragment：residues 138-285	Not recorded	MG MAGNESIUM ION × 40	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；sodium formate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 3.30 Å R-free 0.226
4ZCH Single-chain human APRIL-BAFF-BAFF Heterotrimer Deposited 2015-04-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 140–285（146 aa）	Not recorded	144 TRIS-HYDROXYMETHYL-METHYL-AMMONIUM × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；RESERVOIR SOLUTION : 14% PEG6000 , 1M LiCL , TRIS-HCL pH 8.50	Resolution 2.43 Å R-free 0.234
4ZCH Single-chain human APRIL-BAFF-BAFF Heterotrimer Deposited 2015-04-16	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 140–285（146 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；RESERVOIR SOLUTION : 14% PEG6000 , 1M LiCL , TRIS-HCL pH 8.50	Resolution 2.43 Å R-free 0.234
5Y9J BAFF in complex with belimumab Deposited 2017-08-25	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 134–285（152 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；293 K；0.1 M Tris(hydroxymethyl)aminomethane pH 8.5, 20% (w/v)polyethylene glycol 1,000	Resolution 2.05 Å R-free 0.217
8ZUJ Pentagonal cluster of BAFF-BAFFR ectodomain 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 × 30 PDB declaration: 30-meric	Chain D 134–285（152 aa） Chain E 134–285（152 aa） Chain F 134–285（152 aa） Chain J 134–285（152 aa） Chain K 134–285（152 aa） Chain L 134–285（152 aa） Chain P 134–285（152 aa） Chain Q 134–285（152 aa） Chain R 134–285（152 aa） Chain V 134–285（152 aa） Chain W 134–285（152 aa） Chain X 134–285（152 aa） Chain b 134–285（152 aa） Chain c 134–285（152 aa） Chain d 134–285（152 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.58 Å

11 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TN13B_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 13–164； UniProt 134–285 Author chain B； PDBConstruct 13–164； UniProt 134–285 Author chain C； PDBConstruct 13–164； UniProt 134–285 Author chain J； PDBConstruct 13–164； UniProt 134–285 Author chain K； PDBConstruct 13–164； UniProt 134–285 Author chain L； PDBConstruct 13–164； UniProt 134–285

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6fxn
Deposition date deposition_date	2018-03-09
Structure title title	Crystal structure of human BAFF in complex with Fab fragment of anti-BAFF antibody belimumab
Keywords keywords	Immunology, B cell, cytokine, BAFF, antibody, Proteros, IMMUNE SYSTEM; IMMUNE SYSTEM
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	64.19 Å
Radius of gyration Rg (electron density) rg_electron	64.54 Å
Forward intensity I(0) i0	1929890000.00
Molecular weight molecular_weight	367650.0 kDa
Excluded volume excluded_volume	459070 Å³
Envelope volume envelope_volume	733560 Å³
Hydration-shell volume shell_volume	97140 Å³
Envelope diameter envelope_diameter	242.8 Å
Shell Rg shell_rg	63.93 Å
Envelope Rg envelope_rg	63.28 Å
Shape Rg shape_rg	64.52 Å
Total Rg total_rg	64.58 Å
Total atoms total_atoms	25879
Residues n_residues	3418
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	213.2 Å
Rg (real space) rg_real	64.42 Å
Rg uncertainty (real space) rg_real_error	2.03 Å
I(0) (real space) i0_real	1.9290e+09
I(0) uncertainty (real space) i0_real_error	4.3270e+07
Rg (reciprocal space) rg_reciprocal	63.92 Å
I(0) (reciprocal space) i0_reciprocal	1928000000.0000
Solution quality estimate total_estimate	0.8565
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	80.0 Å
Skewness Skewness skewness	0.405
Kurtosis Kurtosis kurtosis	-0.094
Angular range angular_range	— – 0.1200 Å⁻¹
Current regularization parameter α current_alpha	0.0005
Highest regularization parameter α highest_alpha	55670000.0000
Real-space data points n_real_points	25
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.866; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.533

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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	Tumor necrosis factor ligand superfamily member 13B
Molecular weight formula_weight	18394.9 kDa
Mutation mutation	H218A
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,J,K,L
Atom count atom_count	26179

MRGSHHHHHHGSAVQGPEETVTQDCLQLIADSETPTIQKGSYTFVPWLLSFKRGSALEEKENKILVKETGYFFIYGQVLYTDKTYAMGHLIQRKKVAVFGDELSLVTLFRCIQNMPETLPNNSCYSAGIAKLEEGDELQLAIPRENAQISLDGDVTFFGALKLL

来源 Source

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

Entity 2 Entity 2 polymer

Description description	belimumab heavy chain
Molecular weight formula_weight	23704.6 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,F,H,M,O,Q

QVQLQQSGAEVKKPGSSVRVSCKASGGTFNNNAINWVRQAPGQGLEWMGGIIPMFGTAKYSQNFQGRVAITADESTGTASMELSSLRSEDTAVYYCARSRDLLLFPHHALSPWGRGTMVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKS

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Mus musculus

Entity 3 Entity 3 polymer

Description description	belimumab light chain
Molecular weight formula_weight	22764.9 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,G,I,N,P,R

SSELTQDPAVSVALGQTVRVTCQGDSLRSYYASWYQQKPGQAPVLVIYGKNNRPSGIPDRFSGSSSGNTASLTITGAQAEDEADYYCSSRDSSGNHWVFGGGTELTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Mus musculus

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	270

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7. Fold Classification (SCOP + CATH) 52 domains

SCOP 2.08 (30 domains)

Domain ID domain_id	d6fxna_
Class class	b — All beta proteins
Fold Fold fold	b.22 — TNF-like
Superfamily Superfamily superfamily	b.22.1 — TNF-like
Family Family family	b.22.1.1 — TNF-like

Domain ID domain_id	d6fxnb_
Class class	b — All beta proteins
Fold Fold fold	b.22 — TNF-like
Superfamily Superfamily superfamily	b.22.1 — TNF-like
Family Family family	b.22.1.1 — TNF-like

Domain ID domain_id	d6fxnc_
Class class	b — All beta proteins
Fold Fold fold	b.22 — TNF-like
Superfamily Superfamily superfamily	b.22.1 — TNF-like
Family Family family	b.22.1.1 — TNF-like

Domain ID domain_id	d6fxnd1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d6fxnd2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d6fxne1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d6fxne2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d6fxnf1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d6fxnf2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d6fxng1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d6fxng2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d6fxnh1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d6fxnh2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d6fxni1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d6fxni2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d6fxnj_
Class class	b — All beta proteins
Fold Fold fold	b.22 — TNF-like
Superfamily Superfamily superfamily	b.22.1 — TNF-like
Family Family family	b.22.1.1 — TNF-like

Domain ID domain_id	d6fxnk_
Class class	b — All beta proteins
Fold Fold fold	b.22 — TNF-like
Superfamily Superfamily superfamily	b.22.1 — TNF-like
Family Family family	b.22.1.1 — TNF-like

Domain ID domain_id	d6fxnl_
Class class	b — All beta proteins
Fold Fold fold	b.22 — TNF-like
Superfamily Superfamily superfamily	b.22.1 — TNF-like
Family Family family	b.22.1.1 — TNF-like

Domain ID domain_id	d6fxnm1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d6fxnm2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d6fxnn1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d6fxnn2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d6fxno1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d6fxno2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d6fxnp1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d6fxnp2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d6fxnq1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d6fxnq2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d6fxnr1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d6fxnr2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

CATH v4.4 (22 domains)

Domain ID domain_id	6fxnA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	6fxnB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	6fxnC00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	6fxnD02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6fxnE01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6fxnE02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6fxnF02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6fxnG02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6fxnH02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6fxnI02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6fxnJ00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	6fxnK00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	6fxnL00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	6fxnM02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6fxnN01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6fxnN02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6fxnO02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6fxnP01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6fxnP02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6fxnQ02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6fxnR01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6fxnR02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

▶

8. Citations (1)

▶

Unit-cell length a length_a	135.687 Å
Unit-cell length b length_b	135.499 Å
Unit-cell length c length_c	138.180 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.88 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	138.110 Å
R factor r_factor	0.1911
R_work r_work	0.1908
R_free r_free	0.2313

Crystal structure of human BAFF in complex with Fab fragment of anti-BAFF antibody belimumab

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

Tumor necrosis factor ligand superfamily member 13B

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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 52 domains

SCOP 2.08 (30 domains)

CATH v4.4 (22 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

fit	/app/data/saxs_computation/fx/6fxn/6fxn.fit
pddf	/app/data/pr_computation/fx/6fxn/6fxn.pr.out
profile	/app/data/saxs_computation/fx/6fxn/6fxn.dat