5s7u

XChem group deposition -- Crystal Structure of human ACVR1 in complex with FM010938a

Method: X-RAY DIFFRACTION Dmax: 91.5 Å Quality: EXCELLENT

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

Activin receptor type-1

Homo sapiens

UniProt Q04771

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 201–499 Chain B; UniProt 201–499 Not recorded LU8 4-methyl-3-[4-(1-methylpiperidin-4-yl)phenyl]-5-(3,4,5-trimethoxyphenyl)pyridine × 4 EDO 1,2-ETHANEDIOL × 14 DMS DIMETHYL SULFOXIDE × 2 SO4 SULFATE ION × 6 XGY (4S)-1-methylimidazolidin-4-amine × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6;277 K;0.1M citrate pH 6.0, 1.4M ammonium sulfate, 0.2M sodium/potassium tartrate Resolution 1.59 Å R-free 0.261

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.

84 other PDB entries and 142 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ACVR1_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 3–301; UniProt 201–499 Author chain B; PDBConstruct 3–301; UniProt 201–499

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 5s7u

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5s7u
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5s7u
Deposition date deposition_date2020-12-11
Structure title titleXChem group deposition -- Crystal Structure of human ACVR1 in complex with FM010938a
Keywords keywordsSGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, TRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier29.29
Radius of gyration Rg (electron density) rg_electron28.41
Forward intensity I(0) i070641400.00
Molecular weight molecular_weight66364.0 kDa
Excluded volume excluded_volume83347 ų
Envelope volume envelope_volume103860 ų
Hydration-shell volume shell_volume30832 ų
Envelope diameter envelope_diameter90.5
Shell Rg shell_rg35.28
Envelope Rg envelope_rg28.32
Shape Rg shape_rg28.41
Total Rg total_rg29.12
Total atoms total_atoms4657
Residues n_residues559
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 dmax91.5
Rg (real space) rg_real29.29
Rg uncertainty (real space) rg_real_error0.54
I(0) (real space) i0_real7.0640e+07
I(0) uncertainty (real space) i0_real_error1.1450e+06
Rg (reciprocal space) rg_reciprocal29.29
I(0) (reciprocal space) i0_reciprocal70640000.0000
Solution quality estimate total_estimate0.9017
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary28.8
Skewness Skewness skewness0.255
Kurtosis Kurtosis kurtosis-0.705
Angular range angular_range— – 0.2700 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha15930000.0000
Real-space data points n_real_points55
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.940; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.914

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd5s7ua_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamilyd.144.1 — Protein kinase-like (PK-like)
Family Family familyd.144.1.7 — Protein kinases, catalytic subunit
Domain ID domain_idd5s7ub_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamilyd.144.1 — Protein kinase-like (PK-like)
Family Family familyd.144.1.7 — Protein kinases, catalytic subunit

8. Citations (1)

9. Files and Curves (10)