6y6o

Structure of mature activin A with small molecule 42

Method: X-RAY DIFFRACTION Dmax: 68.6 Å Quality: GOOD

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

Inhibin beta A chain

Homo sapiens

UniProt P08476

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 311–426 Chain B; UniProt 311–426 Not recorded SO4 SULFATE ION × 10 OCK (3~{R})-4-ethyl-3-methyl-3-propyl-1~{H}-1,4-benzodiazepine-2,5-dione × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.4;291 K;1.65 M (NH4)2SO4, 4 % PEG 300, 100 mM Hepes pH 7.4, 2 % DMSO Resolution 2.04 Å R-free 0.254

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.

14 other PDB entries and 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name INHBA_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–116; UniProt 311–426 Author chain B; PDBConstruct 1–116; UniProt 311–426

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

SAXS profile for 6y6o

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6y6o
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6y6o
Deposition date deposition_date2020-02-26
Structure title titleStructure of mature activin A with small molecule 42
Keywords keywordsactivin A, TGF-beta, growth factor, FBDD, inhibitor, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier20.41
Radius of gyration Rg (electron density) rg_electron19.93
Forward intensity I(0) i013862600.00
Molecular weight molecular_weight26216.0 kDa
Excluded volume excluded_volume32087 ų
Envelope volume envelope_volume40129 ų
Hydration-shell volume shell_volume17585 ų
Envelope diameter envelope_diameter71.9
Shell Rg shell_rg25.42
Envelope Rg envelope_rg20.11
Shape Rg shape_rg20.01
Total Rg total_rg20.51
Total atoms total_atoms1819
Residues n_residues226
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax68.6
Rg (real space) rg_real20.42
Rg uncertainty (real space) rg_real_error0.52
I(0) (real space) i0_real1.3860e+07
I(0) uncertainty (real space) i0_real_error1.9810e+05
Rg (reciprocal space) rg_reciprocal20.42
I(0) (reciprocal space) i0_reciprocal13860000.0000
Solution quality estimate total_estimate0.8045
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary23.5
Skewness Skewness skewness0.389
Kurtosis Kurtosis kurtosis-0.204
Angular range angular_range— – 0.3900 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2037000.0000
Real-space data points n_real_points71
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.824; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd6y6oa_
Class classg — Small proteins
Fold Fold foldg.17 — Cystine-knot cytokines
Superfamily Superfamily superfamilyg.17.1 — Cystine-knot cytokines
Family Family familyg.17.1.2 — Transforming growth factor (TGF)-beta
Domain ID domain_idd6y6ob_
Class classg — Small proteins
Fold Fold foldg.17 — Cystine-knot cytokines
Superfamily Superfamily superfamilyg.17.1 — Cystine-knot cytokines
Family Family familyg.17.1.2 — Transforming growth factor (TGF)-beta

8. Citations (1)

9. Files and Curves (10)