3iec

Helicobacter pylori CagA Inhibits PAR1/MARK Family Kinases by Mimicking Host Substrates

Method: X-RAY DIFFRACTION D_max: 141.2 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

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	蛋白异源复合物异源复合物蛋白 × 2 PDB 声明：dimeric（2）与蛋白拷贝数一致	链 A； UniProt 49–363	片段：UNP RESIDUES 49-363	Cytotoxicity-associated immunodominant antigen × 1 （P55980）	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
2	蛋白异源复合物异源复合物蛋白 × 2 PDB 声明：dimeric（2）与蛋白拷贝数一致	链 B； UniProt 49–363	片段：UNP RESIDUES 49-363	Cytotoxicity-associated immunodominant antigen × 1 （P55980）	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
3	蛋白异源复合物异源复合物蛋白 × 2 PDB 声明：dimeric（2）与蛋白拷贝数一致	链 C； UniProt 49–363	片段：UNP RESIDUES 49-363	Cytotoxicity-associated immunodominant antigen × 1 （P55980）	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
4	蛋白异源复合物异源复合物蛋白 × 2 PDB 声明：dimeric（2）与蛋白拷贝数一致	链 D； UniProt 49–363	片段：UNP RESIDUES 49-363	Cytotoxicity-associated immunodominant antigen × 1 （P55980）	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

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 3IEC	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
5EAK Optimization of Microtubule Affinity Regulating Kinase (MARK) Inhibitors with Improved Physical Properties 提交 2015-10-16	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、8 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 5–319； UniProt 49–363 作者链 B； PDB构建体 5–319； UniProt 49–363 作者链 C； PDB构建体 5–319； UniProt 49–363 作者链 D； PDB构建体 5–319； UniProt 49–363

Cytotoxicity-associated immunodominant antigen

Helicobacter pylori

UniProt P55980

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	蛋白异源复合物异源复合物蛋白 × 2 PDB 声明：dimeric（2）与蛋白拷贝数一致	链 E； UniProt 885–1005	片段：UNP RESIDUES 885-1005	Serine/threonine-protein kinase MARK2 × 1 （Q7KZI7）	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
2	蛋白异源复合物异源复合物蛋白 × 2 PDB 声明：dimeric（2）与蛋白拷贝数一致	链 F； UniProt 885–1005	片段：UNP RESIDUES 885-1005	Serine/threonine-protein kinase MARK2 × 1 （Q7KZI7）	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
3	蛋白异源复合物异源复合物蛋白 × 2 PDB 声明：dimeric（2）与蛋白拷贝数一致	链 G； UniProt 885–1005	片段：UNP RESIDUES 885-1005	Serine/threonine-protein kinase MARK2 × 1 （Q7KZI7）	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
4	蛋白异源复合物异源复合物蛋白 × 2 PDB 声明：dimeric（2）与蛋白拷贝数一致	链 H； UniProt 885–1005	片段：UNP RESIDUES 885-1005	Serine/threonine-protein kinase MARK2 × 1 （Q7KZI7）	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

数据库中的同蛋白其他状态

其他 PDB	相对当前条目 3IEC	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
4DVY Crystal structure of the Helicobacter pylori CagA oncoprotein 提交 2012-02-23	构建体不同突变/修饰不同聚集状态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 P 1–876（876 aa）片段：UNP residues 1-876	突变：H131M/L274M	未记录非水小分子	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；8% EtOH, 50mM Tris-HCl, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	分辨率 3.30 Å R-free 0.248
4DVZ Crystal structure of the Helicobacter pylori CagA oncoprotein 提交 2012-02-23	构建体不同聚集状态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 261–829（569 aa）片段：UNP residues 261-829	未记录	未记录非水小分子	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；7% EtOH, 50mM Tris-HCl, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	分辨率 3.19 Å R-free 0.279
4G0H Crystal structure of the N-terminal domain of Helicobacter pylori CagA protein 提交 2012-07-09	构建体不同聚集状态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 1–884（884 aa）片段：UNP residues 1 to 884	未记录	未记录非水小分子	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；20% Ethanol, Na Cacodylate 100mM pH7, NaI 15mM, VAPOR DIFFUSION, HANGING DROP, temperature 293K	分辨率 3.60 Å R-free 0.341
4IRV Structure of the Helicobacter pylori CagA Oncogene Bound to the Human Tumor Suppressor Apoptosis-stimulating Protein of p53-2 提交 2013-01-15	构建体不同突变/修饰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 19–235（217 aa）	非标准单体：是（mmCIF未提供具体位点）	未记录非水小分子	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 8.5；Crystals were grown by vapor diffusion at 25 degrees C using hanging drops formed from mixing a 2ul of the protein complex with 2ul of an equilibration buffer (21% polyethylene glycol (PEG) molecular weight 4 kDa, 200 mM Li2 SO4 , and 100 mM Tris pH 8.5) and 0.6ul of the Silver Bullets additive 43 (Hampton Research HR2-996-43). Significantly higher quality crystals were obtained from selenomethionine-substituted protein complexes and they were used for the final refinement, VAPOR DIFFUSION, HANGING DROP	分辨率 2.04 Å R-free 0.234
4IRV Structure of the Helicobacter pylori CagA Oncogene Bound to the Human Tumor Suppressor Apoptosis-stimulating Protein of p53-2 提交 2013-01-15	构建体不同突变/修饰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 19–235（217 aa）	非标准单体：是（mmCIF未提供具体位点）	未记录非水小分子	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 8.5；Crystals were grown by vapor diffusion at 25 degrees C using hanging drops formed from mixing a 2ul of the protein complex with 2ul of an equilibration buffer (21% polyethylene glycol (PEG) molecular weight 4 kDa, 200 mM Li2 SO4 , and 100 mM Tris pH 8.5) and 0.6ul of the Silver Bullets additive 43 (Hampton Research HR2-996-43). Significantly higher quality crystals were obtained from selenomethionine-substituted protein complexes and they were used for the final refinement, VAPOR DIFFUSION, HANGING DROP	分辨率 2.04 Å R-free 0.234
4IRV Structure of the Helicobacter pylori CagA Oncogene Bound to the Human Tumor Suppressor Apoptosis-stimulating Protein of p53-2 提交 2013-01-15	构建体不同突变/修饰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 19–235（217 aa）	非标准单体：是（mmCIF未提供具体位点）	未记录非水小分子	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 8.5；Crystals were grown by vapor diffusion at 25 degrees C using hanging drops formed from mixing a 2ul of the protein complex with 2ul of an equilibration buffer (21% polyethylene glycol (PEG) molecular weight 4 kDa, 200 mM Li2 SO4 , and 100 mM Tris pH 8.5) and 0.6ul of the Silver Bullets additive 43 (Hampton Research HR2-996-43). Significantly higher quality crystals were obtained from selenomethionine-substituted protein complexes and they were used for the final refinement, VAPOR DIFFUSION, HANGING DROP	分辨率 2.04 Å R-free 0.234
4IRV Structure of the Helicobacter pylori CagA Oncogene Bound to the Human Tumor Suppressor Apoptosis-stimulating Protein of p53-2 提交 2013-01-15	构建体不同突变/修饰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 19–235（217 aa）	非标准单体：是（mmCIF未提供具体位点）	未记录非水小分子	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 8.5；Crystals were grown by vapor diffusion at 25 degrees C using hanging drops formed from mixing a 2ul of the protein complex with 2ul of an equilibration buffer (21% polyethylene glycol (PEG) molecular weight 4 kDa, 200 mM Li2 SO4 , and 100 mM Tris pH 8.5) and 0.6ul of the Silver Bullets additive 43 (Hampton Research HR2-996-43). Significantly higher quality crystals were obtained from selenomethionine-substituted protein complexes and they were used for the final refinement, VAPOR DIFFUSION, HANGING DROP	分辨率 2.04 Å R-free 0.234

共 4 个其他 PDB 条目、7 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	CAGA_HELPY
Isoform	—
PDB实体	2
链与序列区间	作者链 E； PDB构建体 5–125； UniProt 885–1005 作者链 F； PDB构建体 5–125； UniProt 885–1005 作者链 G； PDB构建体 5–125； UniProt 885–1005 作者链 H； PDB构建体 5–125； UniProt 885–1005

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

P(r) 距离分布 P(r) Distribution

下载 Download SAXS (.dat) P(r) (.pr.out) CIF

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2. 结构基本信息 2. Structure Basics

条目编号 entry_id	3iec
沉积日期 deposition_date	2009-07-22
结构标题 title	Helicobacter pylori CagA Inhibits PAR1/MARK Family Kinases by Mimicking Host Substrates
关键词 keywords	;Protein-protein complex, kinase, virulence factor, Alternative promoter usage, ATP-binding, Cell membrane, Developmental protein, Differentiation, Magnesium, Membrane, Metal-binding, Nucleotide-binding, Phosphoprotein, Serine/threonine-protein kinase, Transferase, SIGNALING PROTEIN-TOXIN COMPLEX ;; SIGNALING PROTEIN/TOXIN
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	42.52 Å
回转半径 Rg (电子) rg_electron	42.24 Å
零角强度 I(0) i0	313534000.00
分子量 molecular_weight	150820.0 kDa
排除体积 excluded_volume	191340 Å³
包络体积 envelope_volume	264850 Å³
水化壳体积 shell_volume	53182 Å³
包络直径 envelope_diameter	145.5 Å
壳层 Rg shell_rg	46.55 Å
包络 Rg envelope_rg	41.41 Å
形状 Rg shape_rg	42.22 Å
总 Rg total_rg	42.54 Å
总原子数 total_atoms	10625
残基数 n_residues	1302
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	141.2 Å
Rg (实空间) rg_real	42.52 Å
Rg 误差 (实空间) rg_real_error	1.26 Å
I(0) (实空间) i0_real	3.1350e+08
I(0) 误差 (实空间) i0_real_error	5.7950e+06
Rg (倒空间) rg_reciprocal	42.52 Å
I(0) (倒空间) i0_reciprocal	313500000.0000
解质量估计 total_estimate	0.8886
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	57.3 Å
偏度 Skewness skewness	0.247
峰度 Kurtosis kurtosis	-0.538
角度范围 angular_range	— – 0.1850 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	44800000.0000
实空间数据点数 n_real_points	38
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.910; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.833

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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 (3)

实体 1 Entity 1 polymer

描述 description	Serine/threonine-protein kinase MARK2
分子量 formula_weight	36919.8 kDa
EC 编号 ec_number	2.7.11.1
来源方法 src_method	man
拷贝数 entity_count	4

聚合物 Polymer

聚合物类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	11312

MADLHIGNYRLLKTIGKGNFAKVKLARHILTGKEVAVKIIDKTQLNSSSLQKLFREVRIMKVLNHPNIVKLFEVIETEKTLYLVMEYASGGEVFDYLVAHGWMKEKEARAKFRQIVSAVQYCHQKFIVHRDLKAENLLLDADMNIKIADFGFSNEFTFGNKLDTFCGSPPYAAPELFQGKKYDGPEVDVWSLGVILYTLVSGSLPFDGQNLKELRERVLRGKYRIPFYMSTDCENLLKKFLILNPSKRGTLEQIMKDRWMNVGHEDDELKPYVEPLPDYKDPRRTELMVSMGYTREEIQDSLVGQRYNEVMATYLLLGY

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 polymer

描述 description	Cytotoxicity-associated immunodominant antigen
分子量 formula_weight	13423.1 kDa
来源方法 src_method	man
拷贝数 entity_count	4

聚合物 Polymer

聚合物类型 type	polypeptide(L)
链编号 strand_id	E,F,G,H

GPVDNNNNNGLKNSTEPIYAKVNKKKTGQVASPEEPIYTQVAKKVNAKIDRLNQIASGLGGVGQAAGFPLKRHDKVDDLSKVGLSASPEPIYATIDDLGGPFPLKRHDKVDDLSKVGRSRNQELA

来源 Source

来源生物 organism	Helicobacter pylori
通用名 common_name	Campylobacter pylori
NCBI 分类编号 ncbi_taxonomy_id	210
宿主生物 host_organism	Escherichia coli

实体 3 Entity 3 water

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	687

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7. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d3ieca_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.144 — Protein kinase-like (PK-like)
超家族 Superfamily superfamily	d.144.1 — Protein kinase-like (PK-like)
家族 Family family	d.144.1.0 — automated matches

结构域编号 domain_id	d3iecb_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.144 — Protein kinase-like (PK-like)
超家族 Superfamily superfamily	d.144.1 — Protein kinase-like (PK-like)
家族 Family family	d.144.1.0 — automated matches

结构域编号 domain_id	d3iecc_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.144 — Protein kinase-like (PK-like)
超家族 Superfamily superfamily	d.144.1 — Protein kinase-like (PK-like)
家族 Family family	d.144.1.0 — automated matches

结构域编号 domain_id	d3iecd_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.144 — Protein kinase-like (PK-like)
超家族 Superfamily superfamily	d.144.1 — Protein kinase-like (PK-like)
家族 Family family	d.144.1.0 — automated matches

CATH v4.4 (12 domains)

结构域编号 domain_id	3iecA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	200 — Phosphorylase Kinase; domain 1
同源超家族 H-superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

结构域编号 domain_id	3iecA02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	510 — Transferase(Phosphotransferase); domain 1
同源超家族 H-superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

结构域编号 domain_id	3iecA03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	8 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily	10 — Ubiquitin-associated (UBA) domain

结构域编号 domain_id	3iecB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	200 — Phosphorylase Kinase; domain 1
同源超家族 H-superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

结构域编号 domain_id	3iecB02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	510 — Transferase(Phosphotransferase); domain 1
同源超家族 H-superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

结构域编号 domain_id	3iecB03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	8 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily	10 — Ubiquitin-associated (UBA) domain

结构域编号 domain_id	3iecC01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	200 — Phosphorylase Kinase; domain 1
同源超家族 H-superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

结构域编号 domain_id	3iecC02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	510 — Transferase(Phosphotransferase); domain 1
同源超家族 H-superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

结构域编号 domain_id	3iecC03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	8 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily	10 — Ubiquitin-associated (UBA) domain

结构域编号 domain_id	3iecD01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	200 — Phosphorylase Kinase; domain 1
同源超家族 H-superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

结构域编号 domain_id	3iecD02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	510 — Transferase(Phosphotransferase); domain 1
同源超家族 H-superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

结构域编号 domain_id	3iecD03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	8 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily	10 — Ubiquitin-associated (UBA) domain

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8. 引用文献 (1)

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晶胞边长 a length_a	93.466 Å
晶胞边长 b length_b	93.256 Å
晶胞边长 c length_c	113.955 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	100.94 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	—

分辨率 resolution	2.200 Å
最低分辨率 resolution_low	40.960 Å
R 因子 r_factor	0.2060
R_work r_work	0.2040
R_free r_free	0.2480

fit	/app/data/saxs_computation/ie/3iec/3iec.fit
pddf	/app/data/pr_computation/ie/3iec/3iec.pr.out
profile	/app/data/saxs_computation/ie/3iec/3iec.dat

Helicobacter pylori CagA Inhibits PAR1/MARK Family Kinases by Mimicking Host Substrates

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

Cytotoxicity-associated immunodominant antigen

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 (3)

实体 1 Entity 1 polymer

聚合物 Polymer

来源 Source

实体 2 Entity 2 polymer

聚合物 Polymer

来源 Source

实体 3 Entity 3 water

7. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (4 domains)

CATH v4.4 (12 domains)

8. 引用文献 (1)

9. 文件与曲线 (10)

Files (7)

Curves (3)