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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
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1. 蛋白身份与相关结构 Protein Identity & Related Structures

Serine/threonine-protein kinase MARK2

Homo sapiens

UniProt Q7KZI7

当前结构中的状态

Assembly 聚集状态 构建体 突变与修饰 配体、离子与共同组分 实验方法与环境 结构质量
1 蛋白单体 单体 蛋白 × 1 PDB 声明：monomeric（1） 与蛋白拷贝数一致 链 A； UniProt 47–363 突变：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结晶条件：VAPOR DIFFUSION；pH 6.8；298 K；24% PEG 400, 150 mM LiSO4, 100 mM MES ph 6.8 分辨率 2.10 Å R-free 0.267
2 蛋白单体 单体 蛋白 × 1 PDB 声明：monomeric（1） 与蛋白拷贝数一致 链 B； UniProt 47–363 突变：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结晶条件：VAPOR DIFFUSION；pH 6.8；298 K；24% PEG 400, 150 mM LiSO4, 100 mM MES ph 6.8 分辨率 2.10 Å R-free 0.267

数据库中的同蛋白其他状态

以下每一行都是同一 UniProt 蛋白在另一个 PDB 条目中的 biological assembly， “相对当前条目”直接指出证据层面的不同；没有差异标签表示当前已读取字段一致。

其他 PDB 相对当前条目 8TXY Assembly / 聚集状态 构建体 突变与修饰 配体、离子与非聚合物 实验方法与环境 结构质量
3IEC Helicobacter pylori CagA Inhibits PAR1/MARK Family Kinases by Mimicking Host Substrates 提交 2009-07-22 构建体不同 突变/修饰不同 聚集状态不同 配体/离子不同 实验环境不同 结构质量不同 Assembly 1 蛋白异源复合物 异源复合物；蛋白 × 2 PDB 声明：dimeric
链 A 49–363（315 aa） 片段：UNP RESIDUES 49-363
未记录 未记录非水小分子 X-RAY DIFFRACTION
X-ray结晶条件 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
分辨率 2.20 Å R-free 0.248
3IEC Helicobacter pylori CagA Inhibits PAR1/MARK Family Kinases by Mimicking Host Substrates 提交 2009-07-22 构建体不同 突变/修饰不同 聚集状态不同 配体/离子不同 实验环境不同 结构质量不同 Assembly 2 蛋白异源复合物 异源复合物；蛋白 × 2 PDB 声明：dimeric
链 B 49–363（315 aa） 片段：UNP RESIDUES 49-363
未记录 未记录非水小分子 X-RAY DIFFRACTION
X-ray结晶条件 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
分辨率 2.20 Å R-free 0.248
3IEC Helicobacter pylori CagA Inhibits PAR1/MARK Family Kinases by Mimicking Host Substrates 提交 2009-07-22 构建体不同 突变/修饰不同 聚集状态不同 配体/离子不同 实验环境不同 结构质量不同 Assembly 3 蛋白异源复合物 异源复合物；蛋白 × 2 PDB 声明：dimeric
链 C 49–363（315 aa） 片段：UNP RESIDUES 49-363
未记录 未记录非水小分子 X-RAY DIFFRACTION
X-ray结晶条件 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
分辨率 2.20 Å R-free 0.248
3IEC Helicobacter pylori CagA Inhibits PAR1/MARK Family Kinases by Mimicking Host Substrates 提交 2009-07-22 构建体不同 突变/修饰不同 聚集状态不同 配体/离子不同 实验环境不同 结构质量不同 Assembly 4 蛋白异源复合物 异源复合物；蛋白 × 2 PDB 声明：dimeric
链 D 49–363（315 aa） 片段：UNP RESIDUES 49-363
未记录 未记录非水小分子 X-RAY DIFFRACTION
X-ray结晶条件 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
分辨率 2.20 Å R-free 0.248
5EAK Optimization of Microtubule Affinity Regulating Kinase (MARK) Inhibitors with Improved Physical Properties 提交 2015-10-16 构建体不同 突变/修饰不同 配体/离子不同 实验环境不同 结构质量不同 Assembly 1 蛋白单体 单体；蛋白 × 1 PDB 声明：monomeric
链 A 39–364（326 aa） 片段：CATALYTIC DOMAIN (UNP RESIDUES 39-364)
未记录 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结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.1M BIS-TRIS PH 6.5, 14% PEG3350, 200MM AMM.SULFATE
分辨率 2.80 Å R-free 0.254
5EAK Optimization of Microtubule Affinity Regulating Kinase (MARK) Inhibitors with Improved Physical Properties 提交 2015-10-16 构建体不同 突变/修饰不同 配体/离子不同 实验环境不同 结构质量不同 Assembly 2 蛋白单体 单体；蛋白 × 1 PDB 声明：monomeric
链 B 39–364（326 aa） 片段：CATALYTIC DOMAIN (UNP RESIDUES 39-364)
未记录 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结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.1M BIS-TRIS PH 6.5, 14% PEG3350, 200MM AMM.SULFATE
分辨率 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 提交 2016-07-23 构建体不同 突变/修饰不同 配体/离子不同 实验环境不同 结构质量不同 Assembly 1 蛋白单体 单体；蛋白 × 1 PDB 声明：monomeric
链 A 6–331（326 aa） 片段：UNP residues 6-331
未记录 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结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.1M BIS-TRIS PH 6.5, 14% PEG3350, 200MM AMM.SULFATE
分辨率 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 提交 2016-07-23 构建体不同 突变/修饰不同 配体/离子不同 实验环境不同 结构质量不同 Assembly 2 蛋白单体 单体；蛋白 × 1 PDB 声明：monomeric
链 B 6–331（326 aa） 片段：UNP residues 6-331
未记录 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结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.1M BIS-TRIS PH 6.5, 14% PEG3350, 200MM AMM.SULFATE
分辨率 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 提交 2016-07-23 构建体不同 突变/修饰不同 配体/离子不同 实验环境不同 结构质量不同 Assembly 1 蛋白单体 单体；蛋白 × 1 PDB 声明：monomeric
链 A 6–331（326 aa） 片段：UNP residues 6-331
未记录 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结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.1M BIS-TRIS PH 6.5, 14% PEG3350, 200MM AMM.SULFATE
分辨率 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 提交 2016-07-23 构建体不同 突变/修饰不同 配体/离子不同 实验环境不同 结构质量不同 Assembly 2 蛋白单体 单体；蛋白 × 1 PDB 声明：monomeric
链 B 6–331（326 aa） 片段：UNP residues 6-331
未记录 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结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.1M BIS-TRIS PH 6.5, 14% PEG3350, 200MM AMM.SULFATE
分辨率 3.21 Å R-free 0.290

共 4 个其他 PDB 条目、10 个 assembly。 打开独立比较页并筛选聚集状态

查看构建体与数据证据
UniProt名称 MARK2_HUMAN
Isoform —
PDB实体 1
链与序列区间 作者链 A； PDB构建体 1–317； UniProt 47–363 作者链 B； PDB构建体 1–317； UniProt 47–363

页面优先展示蛋白身份、当前 assembly、共同组分、聚集状态和跨 PDB 结构链接。 链映射与序列区间收在“数据证据”中；数据库内部编号、导入时间和 assembly 操作表达式仅用于维护，因此不在读者页面展示。

SAXS 散射曲线 SAXS Profile

SAXS profile for 8txy

P(r) 距离分布 P(r) Distribution

P(r) distribution for 8txy
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2. 结构基本信息 2. Structure Basics

条目编号 entry_id8txy
沉积日期 deposition_date2023-08-24
结构标题 titleX-ray crystal structure of JRD-SIK1/2i-3 bound to a MARK2-SIK2 chimera
关键词 keywordsKinase, enzyme, chimera, inhibitor, BIOSYNTHETIC PROTEIN; BIOSYNTHETIC PROTEIN
实验方法 methodX-RAY DIFFRACTION
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3. SAXS 参数 (CRYSOL 理论计算) 3. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier29.79 Å
回转半径 Rg (电子) rg_electron28.87 Å
零角强度 I(0) i077008800.00
分子量 molecular_weight71843.0 kDa
排除体积 excluded_volume91214 ų
包络体积 envelope_volume114480 ų
水化壳体积 shell_volume33753 ų
包络直径 envelope_diameter110.0 Å
壳层 Rg shell_rg35.32 Å
包络 Rg envelope_rg28.81 Å
形状 Rg shape_rg28.83 Å
总 Rg total_rg29.63 Å
总原子数 total_atoms5138
残基数 n_residues610
球谐函数阶数 n_harmonics20
q 范围 q_range— – 0.5000 Å−1
数据点数 n_points101
壳层类型 shell_typedirectional
溶剂电子密度 solvent_density0.3340 e/ų
壳层衬度 contrast_shell0.0300 e/ų
CRYSOL 版本 crysol_version4.1.3
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4. P(r) 距离分布 (GNOM 反演) 4. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax104.7 Å
Rg (实空间) rg_real29.84 Å
Rg 误差 (实空间) rg_real_error0.99 Å
I(0) (实空间) i0_real7.7010e+07
I(0) 误差 (实空间) i0_real_error1.1520e+06
Rg (倒空间) rg_reciprocal29.82 Å
I(0) (倒空间) i0_reciprocal77010000.0000
解质量估计 total_estimate0.8676
解质量评级 solution_quality GOOD a GOOD solution
P(r) 峰数 n_peaks2
主峰位置 r_peak_primary33.6 Å
偏度 Skewness skewness0.401
峰度 Kurtosis kurtosis-0.235
角度范围 angular_range— – 0.2650 Å−1
当前正则化参数 α current_alpha0.0000
最高正则化参数 α highest_alpha23810000.0000
实空间数据点数 n_real_points54
GNOM 版本 gnom_version4.1.3
质量判据 quality_criteria AN1: 0.000; Oscil: 0.787; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.934; Smooth: 0.984
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5. 晶体学与实验 5. Crystallography & Experiment

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6. 实体与聚合物信息 Entities & Polymers (5)

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8. 引用文献 (1)

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9. 文件与曲线 (10)