SAXSdb — 1kld

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

TRANSFORMING GROWTH FACTOR-BETA 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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 279–390 Chain B； UniProt 279–390	Not recorded	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 4.2	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 1KLD	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1KLA SOLUTION STRUCTURE OF TGF-B1, NMR, MODELS 1-17 OF 33 STRUCTURES Deposited 1996-01-16	Parsed fields agree	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 279–390（112 aa） Chain B 279–390（112 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4.2	Resolution not provided
1KLC SOLUTION STRUCTURE OF TGF-B1, NMR, MINIMIZED AVERAGE STRUCTURE Deposited 1996-01-16	Parsed fields agree	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 279–390（112 aa） Chain B 279–390（112 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4.2	Resolution not provided
3KFD Ternary complex of TGF-b1 reveals isoform-specific ligand recognition and receptor recruitment in the superfamily Deposited 2009-10-27	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 279–390（112 aa） Chain B 279–390（112 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；298 K；8-15% Peg 4000-8000, pH 7.0, VAPOR DIFFUSION, temperature 298K	Resolution 3.00 Å R-free 0.268
3KFD Ternary complex of TGF-b1 reveals isoform-specific ligand recognition and receptor recruitment in the superfamily Deposited 2009-10-27	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain C 279–390（112 aa） Chain D 279–390（112 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；298 K；8-15% Peg 4000-8000, pH 7.0, VAPOR DIFFUSION, temperature 298K	Resolution 3.00 Å R-free 0.268
3KFD Ternary complex of TGF-b1 reveals isoform-specific ligand recognition and receptor recruitment in the superfamily Deposited 2009-10-27	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 279–390（112 aa） Chain B 279–390（112 aa） Chain C 279–390（112 aa） Chain D 279–390（112 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；298 K；8-15% Peg 4000-8000, pH 7.0, VAPOR DIFFUSION, temperature 298K	Resolution 3.00 Å R-free 0.268
4KV5 scFv GC1009 in complex with TGF-beta1. Deposited 2013-05-22	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 279–390（112 aa） Fragment：unp residues 279-390 Chain D 279–390（112 aa） Fragment：unp residues 279-390	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5；294 K；16% PEG 4K, 0.1 M citrate, 4% 2-propanol , pH 5.0, VAPOR DIFFUSION, temperature 294K	Resolution 3.00 Å R-free 0.300
4KV5 scFv GC1009 in complex with TGF-beta1. Deposited 2013-05-22	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 279–390（112 aa） Fragment：unp residues 279-390 Chain B 279–390（112 aa） Fragment：unp residues 279-390	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5；294 K；16% PEG 4K, 0.1 M citrate, 4% 2-propanol , pH 5.0, VAPOR DIFFUSION, temperature 294K	Resolution 3.00 Å R-free 0.300
5FFO Integrin alpha V beta 6 in complex with pro-TGF-beta Deposited 2015-12-18	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 × 8 PDB declaration: octameric	Chain C 34–390（357 aa） Fragment：UNP residues 34-390 Chain D 34–390（357 aa） Fragment：UNP residues 34-390 Chain G 34–390（357 aa） Fragment：UNP residues 34-390 Chain H 34–390（357 aa） Fragment：UNP residues 34-390	Not recorded	CA CALCIUM ION × 8 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 MN MANGANESE (II) ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；8% PEG8000 0.1M Immidazole	Resolution 3.49 Å R-free 0.277
5VQP Crystal structure of human pro-TGF-beta1 Deposited 2017-05-09	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 30–390（361 aa）	Mutation：C4S,N107Q,N147Q	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.3；289 K；100 mM MES pH6.3, 1.68 M Ammonium Sulfate, 11% Dioxane	Resolution 2.90 Å R-free 0.293
6GFF Structure of GARP (LRRC32) in complex with latent TGF-beta1 and MHG-8 Fab Deposited 2018-04-30	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric	Chain A 30–278（249 aa） Fragment：LAP Chain B 279–390（112 aa） Fragment：Mature Chain C 30–278（249 aa） Fragment：LAP Chain D 279–390（112 aa） Fragment：Mature	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；15% (w/v) PEG4000, 0.1 M HEPES pH 6.75	Resolution 3.10 Å R-free 0.268
6GFF Structure of GARP (LRRC32) in complex with latent TGF-beta1 and MHG-8 Fab Deposited 2018-04-30	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 7 PDB declaration: heptameric	Chain E 30–278（249 aa） Fragment：LAP Chain F 279–390（112 aa） Fragment：Mature Chain G 30–278（249 aa） Fragment：LAP Chain H 279–390（112 aa） Fragment：Mature	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；15% (w/v) PEG4000, 0.1 M HEPES pH 6.75	Resolution 3.10 Å R-free 0.268
6P7J Crystal structure of Latency Associated Peptide unbound to TGF-beta1 Deposited 2019-06-05	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 30–278（249 aa）	Mutation：R249A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions BATCH MODE；pH 4.6；293 K；Reservoir composition: 20% PEG3350, 300 mM NaAc pH 4.6	Resolution 3.50 Å R-free 0.322
7Y1R Human L-TGF-beta1 in complex with the anchor protein LRRC33 Deposited 2022-06-08	Different construct 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 30–390（361 aa） Chain B 30–390（361 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.01 Å
7Y1T Complex of integrin alphaV/beta8 and L-TGF-beta1 at a ratio of 1:2 Deposited 2022-06-08	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 D 30–390（361 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 CA CALCIUM ION × 5 MN MANGANESE (II) ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.24 Å
8C7H Cryo-EM Map of the latTGF-beta LHG-10 Fab complex Deposited 2023-01-16	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric	Chain A 30–278（249 aa） Fragment：LAP Chain B 279–390（112 aa） Fragment：Mature Chain C 30–278（249 aa） Fragment：LAP Chain D 279–390（112 aa） Fragment：Mature	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å
8REW CryoEM structure of human GARP-lTGFbeta1 in complex with a Fab fragment derived from an activating antibody. Deposited 2023-12-12	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 × 9 PDB declaration: nonameric	Chain A 1–390（390 aa） Fragment：LAP Chain B 1–390（390 aa） Fragment：LAP Chain C 1–390（390 aa） Fragment：LAP Chain D 1–390（390 aa） Fragment：LAP	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.98 Å
8UDZ The Structure of LTBP-49247 Fab Bound to TGFbeta1 Small Latent Complex Deposited 2023-09-29	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 × 6 PDB declaration: hexameric	Chain A 30–390（361 aa） Chain B 30–390（361 aa）	Mutation：C33S, R278A Mutation：C33S, R278A	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4；293 K；15% PEG 3350, 12% Tacsimate (pH 4.0), 10 mM Magnesium Chloride	Resolution 2.21 Å R-free 0.264
8VSC L-TGF-b1/GARP Deposited 2024-01-23	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–390（390 aa） Chain B 1–390（390 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
9FDY Betaglycan Orphan Domain (ratBGo) in complex with TGF-b1 and extracellular domain of TGFBRII Deposited 2024-05-17	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 279–390（112 aa） Fragment：Mature Chain B 279–390（112 aa） Fragment：Mature	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
9FKP Zebrafish Betaglycan Orphan Domain (zfBGo) in complex with TGF-b1 and extracellular domain of TGFBRII Deposited 2024-06-03	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 279–390（112 aa） Fragment：Mature Chain B 279–390（112 aa） Fragment：Mature	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.72 Å
9VJJ Crystal Structure of human Latent TGF-beta1 in complex with SOF10 Deposited 2025-06-20	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 30–390（361 aa） Chain B 30–390（361 aa）	Mutation：C33S Mutation：C33S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；0.2M Sodium acetate trihydrate, 0.1M Imidazole hydrochloride (pH 8.0), 10.0% w/v Polyethylene glycol 8000	Resolution 2.48 Å R-free 0.310

17 other PDB entries and 21 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TGFB1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–112； UniProt 279–390 Author chain B； PDBConstruct 1–112； UniProt 279–390

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	1kld
Deposition date deposition_date	1996-01-16
Structure title title	SOLUTION STRUCTURE OF TGF-B1, NMR, MODELS 18-33 OF 33 STRUCTURES
Keywords keywords	GROWTH FACTOR, MITOGEN, GLYCOPROTEIN; GROWTH FACTOR
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	19.42 Å
Radius of gyration Rg (electron density) rg_electron	20.16 Å
Forward intensity I(0) i0	2275270000.00
Molecular weight molecular_weight	409560.0 kDa
Excluded volume excluded_volume	513200 Å³
Envelope volume envelope_volume	57533 Å³
Hydration-shell volume shell_volume	21894 Å³
Envelope diameter envelope_diameter	90.8 Å
Shell Rg shell_rg	28.92 Å
Envelope Rg envelope_rg	24.01 Å
Shape Rg shape_rg	20.23 Å
Total Rg total_rg	20.03 Å
Total atoms total_atoms	56576
Residues n_residues	3584
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	52.0 Å
Rg (real space) rg_real	18.14 Å
Rg uncertainty (real space) rg_real_error	0.09 Å
I(0) (real space) i0_real	2.1640e+09
I(0) uncertainty (real space) i0_real_error	2.2530e+07
Rg (reciprocal space) rg_reciprocal	19.61 Å
I(0) (reciprocal space) i0_reciprocal	2275000000.0000
Solution quality estimate total_estimate	0.6867
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	21.2 Å
Skewness Skewness skewness	0.318
Kurtosis Kurtosis kurtosis	-0.441
Angular range angular_range	— – 0.4100 Å⁻¹
Current regularization parameter α current_alpha	2.9070
Highest regularization parameter α highest_alpha	1015000.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.004; Oscil: 0.990; Stabil: 0.987; Sysdev: 0.000; Positv: 1.000; Valcen: 0.997; 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) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1klda_
Class class	g — Small proteins
Fold Fold fold	g.17 — Cystine-knot cytokines
Superfamily Superfamily superfamily	g.17.1 — Cystine-knot cytokines
Family Family family	g.17.1.2 — Transforming growth factor (TGF)-beta

Domain ID domain_id	d1kldb_
Class class	g — Small proteins
Fold Fold fold	g.17 — Cystine-knot cytokines
Superfamily Superfamily superfamily	g.17.1 — Cystine-knot cytokines
Family Family family	g.17.1.2 — Transforming growth factor (TGF)-beta

CATH v4.4 (2 domains)

Domain ID domain_id	1kldA00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	90 — Cystine Knot Cytokines, subunit B
Homologous superfamily homologous superfamily	10 — Cystine-knot cytokines

Domain ID domain_id	1kldB00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	90 — Cystine Knot Cytokines, subunit B
Homologous superfamily homologous superfamily	10 — Cystine-knot cytokines

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	1

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

Description description	TRANSFORMING GROWTH FACTOR-BETA 1
Molecular weight formula_weight	12809.8 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	56576

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	Cricetulus griseus

SOLUTION STRUCTURE OF TGF-B1, NMR, MODELS 18-33 OF 33 STRUCTURES

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

TRANSFORMING GROWTH FACTOR-BETA 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

Unit cell Unit Cell

Symmetry Symmetry

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

fit	/app/data/saxs_computation/kl/1kld/1kld.fit
pddf	/app/data/pr_computation/kl/1kld/1kld.pr.out
profile	/app/data/saxs_computation/kl/1kld/1kld.dat