6t8n

Crystal structure of the ACVR1 (ALK2) kinase in complex with the compound M4K3007

Method: X-RAY DIFFRACTION Dmax: 86.9 Å Quality: EXCELLENT

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

Activin receptor type I

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 monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 201–499 Mutation:Q207D EDO 1,2-ETHANEDIOL × 1 SO4 SULFATE ION × 1 TLA L(+)-TARTARIC ACID × 1 MVE cyclopropyl-[4-[6-[5-(4-ethoxy-1-propan-2-yl-piperidin-4-yl)pyridin-2-yl]pyrrolo[1,2-b]pyridazin-4-yl]piperazin-1-yl]methanone × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5.5;277 K;0.1M citrate pH 5.5 1.2M ammonium sulfate 0.4M sodium/potassium tartrate Resolution 1.77 Å R-free 0.237
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 201–499 Mutation:Q207D SO4 SULFATE ION × 3 MVE cyclopropyl-[4-[6-[5-(4-ethoxy-1-propan-2-yl-piperidin-4-yl)pyridin-2-yl]pyrrolo[1,2-b]pyridazin-4-yl]piperazin-1-yl]methanone × 1 DMS DIMETHYL SULFOXIDE × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5.5;277 K;0.1M citrate pH 5.5 1.2M ammonium sulfate 0.4M sodium/potassium tartrate Resolution 1.77 Å R-free 0.237

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 141 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 6t8n

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6t8n
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6t8n
Deposition date deposition_date2019-10-24
Structure title titleCrystal structure of the ACVR1 (ALK2) kinase in complex with the compound M4K3007
Keywords keywordsKINASE, BMP, INHIBITOR, SIGNALLING, 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_guinier27.19
Radius of gyration Rg (electron density) rg_electron26.19
Forward intensity I(0) i075243000.00
Molecular weight molecular_weight68185.0 kDa
Excluded volume excluded_volume85461 ų
Envelope volume envelope_volume102570 ų
Hydration-shell volume shell_volume32240 ų
Envelope diameter envelope_diameter92.6
Shell Rg shell_rg33.88
Envelope Rg envelope_rg26.10
Shape Rg shape_rg26.20
Total Rg total_rg26.94
Total atoms total_atoms9264
Residues n_residues586
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 dmax86.9
Rg (real space) rg_real27.12
Rg uncertainty (real space) rg_real_error0.49
I(0) (real space) i0_real7.5240e+07
I(0) uncertainty (real space) i0_real_error9.6470e+05
Rg (reciprocal space) rg_reciprocal27.15
I(0) (reciprocal space) i0_reciprocal75240000.0000
Solution quality estimate total_estimate0.9011
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary31.5
Skewness Skewness skewness0.270
Kurtosis Kurtosis kurtosis-0.443
Angular range angular_range— – 0.2900 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha15370000.0000
Real-space data points n_real_points59
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.915; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.965

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd6t8na_
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_idd6t8nb_
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

CATH v4.4 (4 domains)

Domain ID domain_id6t8nA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
Domain ID domain_id6t8nA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
Domain ID domain_id6t8nB01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
Domain ID domain_id6t8nB02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1

8. Citations (1)

9. Files and Curves (10)