SAXSdb — 5kz7

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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

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 6–331	片段：UNP residues 6-331	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
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 6–331	片段：UNP residues 6-331	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

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 5KZ7	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	构建体不同配体/离子不同结构质量不同	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	构建体不同配体/离子不同结构质量不同	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
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	配体/离子不同结构质量不同	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	配体/离子不同结构质量不同	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
8TXY X-ray crystal structure of JRD-SIK1/2i-3 bound to a MARK2-SIK2 chimera 提交 2023-08-24	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 47–363（317 aa）	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
8TXY X-ray crystal structure of JRD-SIK1/2i-3 bound to a MARK2-SIK2 chimera 提交 2023-08-24	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 47–363（317 aa）	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

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	Q7KZI7-7
PDB实体	1
链与序列区间	作者链 A； PDB构建体 21–346； UniProt 6–331 作者链 B； PDB构建体 21–346； UniProt 6–331

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。

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2. 结构基本信息 2. Structure Basics

条目编号 entry_id	5kz7
沉积日期 deposition_date	2016-07-23
结构标题 title	Mark2 complex with 7-[(1S)-1-(4-fluorophenyl)ethyl]-5,5-dimethyl-2-(3-pyridylamino)pyrrolo[2,3-d]pyrimidin-6-one
关键词 keywords	Mark, Serine/threonine-protein kinase, Transferase-Transferase Inhibitor complex; Transferase/Transferase Inhibitor
实验方法 method	X-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_guinier	29.80 Å
回转半径 Rg (电子) rg_electron	28.93 Å
零角强度 I(0) i0	69325600.00
分子量 molecular_weight	68109.0 kDa
排除体积 excluded_volume	86455 Å³
包络体积 envelope_volume	109110 Å³
水化壳体积 shell_volume	32435 Å³
包络直径 envelope_diameter	107.7 Å
壳层 Rg shell_rg	35.16 Å
包络 Rg envelope_rg	28.49 Å
形状 Rg shape_rg	28.91 Å
总 Rg total_rg	29.64 Å
总原子数 total_atoms	4799
残基数 n_residues	592
球谐函数阶数 n_harmonics	20
q 范围 q_range	— – 0.5000 Å⁻¹
数据点数 n_points	101
壳层类型 shell_type	directional
溶剂电子密度 solvent_density	0.3340 e/Å³
壳层衬度 contrast_shell	0.0300 e/Å³
CRYSOL 版本 crysol_version	4.1.3

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4. P(r) 距离分布 (GNOM 反演) 4. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	102.7 Å
Rg (实空间) rg_real	29.84 Å
Rg 误差 (实空间) rg_real_error	0.88 Å
I(0) (实空间) i0_real	6.9330e+07
I(0) 误差 (实空间) i0_real_error	1.0370e+06
Rg (倒空间) rg_reciprocal	29.83 Å
I(0) (倒空间) i0_reciprocal	69320000.0000
解质量估计 total_estimate	0.8748
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	34.9 Å
偏度 Skewness skewness	0.371
峰度 Kurtosis kurtosis	-0.279
角度范围 angular_range	— – 0.2650 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	14690000.0000
实空间数据点数 n_real_points	54
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.840; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.952; Smooth: 0.898

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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 (2)

实体 1 Entity 1 polymer

描述 description	Serine/threonine-protein kinase MARK2
分子量 formula_weight	40056.1 kDa
EC 编号 ec_number	2.7.11.1,2.7.11.26
来源方法 src_method	man
拷贝数 entity_count	2

聚合物 Polymer

聚合物类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	4799

MAHNHRHKHADYKDDDDKKLNSATSADEQPHIGNYRLLKTIGKGNFAKVKLARHILTGKEVAVKIIDKTQLNSSSLQKLFREVRIMKVLNHPNIVKLFEVIETEKTLYLVMEYASGGEVFDYLVAHGRMKEKEARAKFRQIVSAVQYCHQKFIVHRDLKAENLLLDADMNIKIADFGFSNEFTFGNKLDTFCGSPPYAAPELFQGKKYDGPEVDVWSLGVILYTLVSGSLPFDGQNLKELRERVLRGKYRIPFYMSTDCENLLKKFLILNPSKRGTLEQIMKDRWMNVGHEDDELKPYVEPLPDYKDPRRTELMVSMGYTREEIQDSLVGQRYNEVMATYLLLGYK

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

实体 2 Entity 2 non-polymer

描述 description	7-[(1~{S})-1-(4-fluorophenyl)ethyl]-5,5-dimethyl-2-(pyridin-3-ylamino)pyrrolo[2,3-d]pyrimidin-6-one
分子量 formula_weight	377.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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8. 引用文献 (1)

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晶胞边长 a length_a	119.350 Å
晶胞边长 b length_b	119.350 Å
晶胞边长 c length_c	98.738 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.00 °
晶胞夹角 γ angle_gamma	120.00 °
晶胞分子数 Z z_pdb	12

空间群 space_group	P 61
空间群编号 int_tables_number	169
晶系 crystal_system	—

分辨率 resolution	3.200 Å
最低分辨率 resolution_low	19.530 Å
R 因子 r_factor	0.2255
R_work r_work	0.2220
R_free r_free	0.2934

fit	/app/data/saxs_computation/kz/5kz7/5kz7.fit
pddf	/app/data/pr_computation/kz/5kz7/5kz7.pr.out
profile	/app/data/saxs_computation/kz/5kz7/5kz7.dat

Mark2 complex with 7-[(1S)-1-(4-fluorophenyl)ethyl]-5,5-dimethyl-2-(3-pyridylamino)pyrrolo[2,3-d]pyrimidin-6-one

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

Serine/threonine-protein kinase MARK2

当前结构中的状态

数据库中的同蛋白其他状态

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

2. 结构基本信息 2. Structure Basics

3. SAXS 参数 (CRYSOL 理论计算) 3. SAXS Parameters (CRYSOL)

4. P(r) 距离分布 (GNOM 反演) 4. P(r) Analysis (GNOM)

5. 晶体学与实验 5. Crystallography & Experiment

晶胞参数 Unit Cell

对称性 Symmetry

精修参数 Refinement

衍射实验 Diffraction

6. 实体与聚合物信息 Entities & Polymers (2)

实体 1 Entity 1 polymer

聚合物 Polymer

来源 Source

实体 2 Entity 2 non-polymer

8. 引用文献 (1)

9. 文件与曲线 (10)

Files (7)

Curves (3)