← Back to search
8txy

X-ray crystal structure of JRD-SIK1/2i-3 bound to a MARK2-SIK2 chimera

Method: X-RAY DIFFRACTION Dmax: 104.7 Å Quality: GOOD
▼

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

Serine/threonine-protein kinase MARK2

Homo sapiens

UniProt Q7KZI7

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 47–363 Mutation：I59L, K66V V81I, L97I, V113I, M129T, S133K, G134N , S197G PEG DI(HYDROXYETHYL)ETHER × 2 SJ0 N-[(5P,8R)-5-(2-cyano-5-{[(3R)-1-methylpyrrolidin-3-yl]methoxy}pyridin-4-yl)pyrazolo[1,5-a]pyridin-2-yl]cyclopropanecarboxamide × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 6.8；298 K；24% PEG 400, 150 mM LiSO4, 100 mM MES ph 6.8 Resolution 2.10 Å R-free 0.267
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 47–363 Mutation：I59L, K66V V81I, L97I, V113I, M129T, S133K, G134N , S197G PEG DI(HYDROXYETHYL)ETHER × 1 SJ0 N-[(5P,8R)-5-(2-cyano-5-{[(3R)-1-methylpyrrolidin-3-yl]methoxy}pyridin-4-yl)pyrazolo[1,5-a]pyridin-2-yl]cyclopropanecarboxamide × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 6.8；298 K；24% PEG 400, 150 mM LiSO4, 100 mM MES ph 6.8 Resolution 2.10 Å R-free 0.267

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 8TXY Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3IEC Helicobacter pylori CagA Inhibits PAR1/MARK Family Kinases by Mimicking Host Substrates Deposited 2009-07-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 49–363（315 aa） Fragment：UNP RESIDUES 49-363
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；296 K；Initial crystals were grown by vapor diffusion using hanging drops formed from mixing a 2:1 volume ratio of the protein complex with an equilibration buffer consisting of 22.5-25% polyethylene glycol (PEG) molecular weight 3350 Da, 300 mM Li2SO4, and 100 mM Bis-Tris pH 5.8-6.2, at 23 C. Higher quality crystals were obtained by micro-seeding and addition of 5% PEG 400 as an additive. For cryoprotection crystals where transferred directly into a buffer with a 25% PEG 3350 Da, 5-10% PEG 400 Da, 300mM Li2SO4, 100mM Bis-Tris pH 5.8-6.2, 7.5% glycerol, and flash-cooled immediately afterward to -160 C. , VAPOR DIFFUSION, HANGING DROP, temperature 296K
Resolution 2.20 Å R-free 0.248
3IEC Helicobacter pylori CagA Inhibits PAR1/MARK Family Kinases by Mimicking Host Substrates Deposited 2009-07-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 49–363（315 aa） Fragment：UNP RESIDUES 49-363
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；296 K；Initial crystals were grown by vapor diffusion using hanging drops formed from mixing a 2:1 volume ratio of the protein complex with an equilibration buffer consisting of 22.5-25% polyethylene glycol (PEG) molecular weight 3350 Da, 300 mM Li2SO4, and 100 mM Bis-Tris pH 5.8-6.2, at 23 C. Higher quality crystals were obtained by micro-seeding and addition of 5% PEG 400 as an additive. For cryoprotection crystals where transferred directly into a buffer with a 25% PEG 3350 Da, 5-10% PEG 400 Da, 300mM Li2SO4, 100mM Bis-Tris pH 5.8-6.2, 7.5% glycerol, and flash-cooled immediately afterward to -160 C. , VAPOR DIFFUSION, HANGING DROP, temperature 296K
Resolution 2.20 Å R-free 0.248
3IEC Helicobacter pylori CagA Inhibits PAR1/MARK Family Kinases by Mimicking Host Substrates Deposited 2009-07-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 49–363（315 aa） Fragment：UNP RESIDUES 49-363
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；296 K；Initial crystals were grown by vapor diffusion using hanging drops formed from mixing a 2:1 volume ratio of the protein complex with an equilibration buffer consisting of 22.5-25% polyethylene glycol (PEG) molecular weight 3350 Da, 300 mM Li2SO4, and 100 mM Bis-Tris pH 5.8-6.2, at 23 C. Higher quality crystals were obtained by micro-seeding and addition of 5% PEG 400 as an additive. For cryoprotection crystals where transferred directly into a buffer with a 25% PEG 3350 Da, 5-10% PEG 400 Da, 300mM Li2SO4, 100mM Bis-Tris pH 5.8-6.2, 7.5% glycerol, and flash-cooled immediately afterward to -160 C. , VAPOR DIFFUSION, HANGING DROP, temperature 296K
Resolution 2.20 Å R-free 0.248
3IEC Helicobacter pylori CagA Inhibits PAR1/MARK Family Kinases by Mimicking Host Substrates Deposited 2009-07-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 49–363（315 aa） Fragment：UNP RESIDUES 49-363
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；296 K；Initial crystals were grown by vapor diffusion using hanging drops formed from mixing a 2:1 volume ratio of the protein complex with an equilibration buffer consisting of 22.5-25% polyethylene glycol (PEG) molecular weight 3350 Da, 300 mM Li2SO4, and 100 mM Bis-Tris pH 5.8-6.2, at 23 C. Higher quality crystals were obtained by micro-seeding and addition of 5% PEG 400 as an additive. For cryoprotection crystals where transferred directly into a buffer with a 25% PEG 3350 Da, 5-10% PEG 400 Da, 300mM Li2SO4, 100mM Bis-Tris pH 5.8-6.2, 7.5% glycerol, and flash-cooled immediately afterward to -160 C. , VAPOR DIFFUSION, HANGING DROP, temperature 296K
Resolution 2.20 Å R-free 0.248
5EAK Optimization of Microtubule Affinity Regulating Kinase (MARK) Inhibitors with Improved Physical Properties Deposited 2015-10-16 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 39–364（326 aa） Fragment：CATALYTIC DOMAIN (UNP RESIDUES 39-364)
Not recorded 24R N-[(1S,2R)-2-aminocyclohexyl]-4-[6-(1-methyl-1H-pyrazol-4-yl)pyrazolo[1,5-a]pyrimidin-3-yl]thiophene-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.1M BIS-TRIS PH 6.5, 14% PEG3350, 200MM AMM.SULFATE
Resolution 2.80 Å R-free 0.254
5EAK Optimization of Microtubule Affinity Regulating Kinase (MARK) Inhibitors with Improved Physical Properties Deposited 2015-10-16 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 39–364（326 aa） Fragment：CATALYTIC DOMAIN (UNP RESIDUES 39-364)
Not recorded 24R N-[(1S,2R)-2-aminocyclohexyl]-4-[6-(1-methyl-1H-pyrazol-4-yl)pyrazolo[1,5-a]pyrimidin-3-yl]thiophene-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.1M BIS-TRIS PH 6.5, 14% PEG3350, 200MM AMM.SULFATE
Resolution 2.80 Å R-free 0.254
5KZ7 Mark2 complex with 7-[(1S)-1-(4-fluorophenyl)ethyl]-5,5-dimethyl-2-(3-pyridylamino)pyrrolo[2,3-d]pyrimidin-6-one Deposited 2016-07-23 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 6–331（326 aa） Fragment：UNP residues 6-331
Not recorded 6Z2 7-[(1~{S})-1-(4-fluorophenyl)ethyl]-5,5-dimethyl-2-(pyridin-3-ylamino)pyrrolo[2,3-d]pyrimidin-6-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.1M BIS-TRIS PH 6.5, 14% PEG3350, 200MM AMM.SULFATE
Resolution 3.20 Å R-free 0.293
5KZ7 Mark2 complex with 7-[(1S)-1-(4-fluorophenyl)ethyl]-5,5-dimethyl-2-(3-pyridylamino)pyrrolo[2,3-d]pyrimidin-6-one Deposited 2016-07-23 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 6–331（326 aa） Fragment：UNP residues 6-331
Not recorded 6Z2 7-[(1~{S})-1-(4-fluorophenyl)ethyl]-5,5-dimethyl-2-(pyridin-3-ylamino)pyrrolo[2,3-d]pyrimidin-6-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.1M BIS-TRIS PH 6.5, 14% PEG3350, 200MM AMM.SULFATE
Resolution 3.20 Å R-free 0.293
5KZ8 Mark2 complex with 7-[(1S)-1-(4-fluorophenyl)ethyl]-5,5-dimethyl-2-(3-pyridylamino)pyrrolo[2,3-d]pyrimidin-6-one Deposited 2016-07-23 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 6–331（326 aa） Fragment：UNP residues 6-331
Not recorded 6Z5 5,5-dimethyl-7-[(1~{S})-4-oxidanyl-1~{H}-inden-1-yl]-2-phenylazanyl-pyrrolo[2,3-d]pyrimidin-6-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.1M BIS-TRIS PH 6.5, 14% PEG3350, 200MM AMM.SULFATE
Resolution 3.21 Å R-free 0.290
5KZ8 Mark2 complex with 7-[(1S)-1-(4-fluorophenyl)ethyl]-5,5-dimethyl-2-(3-pyridylamino)pyrrolo[2,3-d]pyrimidin-6-one Deposited 2016-07-23 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 6–331（326 aa） Fragment：UNP residues 6-331
Not recorded 6Z5 5,5-dimethyl-7-[(1~{S})-4-oxidanyl-1~{H}-inden-1-yl]-2-phenylazanyl-pyrrolo[2,3-d]pyrimidin-6-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.1M BIS-TRIS PH 6.5, 14% PEG3350, 200MM AMM.SULFATE
Resolution 3.21 Å R-free 0.290

4 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MARK2_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–317； UniProt 47–363 Author chain B； PDBConstruct 1–317； UniProt 47–363

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 8txy

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8txy
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id8txy
Deposition date deposition_date2023-08-24
Structure title titleX-ray crystal structure of JRD-SIK1/2i-3 bound to a MARK2-SIK2 chimera
Keywords keywordsKinase, enzyme, chimera, inhibitor, BIOSYNTHETIC PROTEIN; BIOSYNTHETIC PROTEIN
Experimental Method methodX-RAY DIFFRACTION
▼

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

Radius of gyration Rg (Guinier) rg_guinier29.79 Å
Radius of gyration Rg (electron density) rg_electron28.87 Å
Forward intensity I(0) i077008800.00
Molecular weight molecular_weight71843.0 kDa
Excluded volume excluded_volume91214 ų
Envelope volume envelope_volume114480 ų
Hydration-shell volume shell_volume33753 ų
Envelope diameter envelope_diameter110.0 Å
Shell Rg shell_rg35.32 Å
Envelope Rg envelope_rg28.81 Å
Shape Rg shape_rg28.83 Å
Total Rg total_rg29.63 Å
Total atoms total_atoms5138
Residues n_residues610
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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 dmax104.7 Å
Rg (real space) rg_real29.84 Å
Rg uncertainty (real space) rg_real_error0.99 Å
I(0) (real space) i0_real7.7010e+07
I(0) uncertainty (real space) i0_real_error1.1520e+06
Rg (reciprocal space) rg_reciprocal29.82 Å
I(0) (reciprocal space) i0_reciprocal77010000.0000
Solution quality estimate total_estimate0.8676
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary33.6 Å
Skewness Skewness skewness0.401
Kurtosis Kurtosis kurtosis-0.235
Angular range angular_range— – 0.2650 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha23810000.0000
Real-space data points n_real_points54
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.787; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.934; Smooth: 0.984
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (5)

▶

8. Citations (1)

▶

9. Files and Curves (10)