1lkx

MOTOR DOMAIN OF MYOE, A CLASS-I MYOSIN

Method: X-RAY DIFFRACTION D_max: 197.2 Å Quality: GOOD

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

MYOSIN IE HEAVY CHAIN

Dictyostelium discoideum

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 1–697	片段：Motor Domain	MG MAGNESIUM ION × 1 VO4 VANADATE ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION, HANGING DROP；pH 7.2；289 K；11% PEG 8K, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 289K	分辨率 3.00 Å R-free 0.273
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 1–697	片段：Motor Domain	MG MAGNESIUM ION × 1 VO4 VANADATE ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION, HANGING DROP；pH 7.2；289 K；11% PEG 8K, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 289K	分辨率 3.00 Å R-free 0.273
3	蛋白单体单体蛋白 × 1 PDB 声明：monomeric（1）与蛋白拷贝数一致	链 C； UniProt 1–697	片段：Motor Domain	MG MAGNESIUM ION × 1 VO4 VANADATE ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION, HANGING DROP；pH 7.2；289 K；11% PEG 8K, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 289K	分辨率 3.00 Å R-free 0.273
4	蛋白单体单体蛋白 × 1 PDB 声明：monomeric（1）与蛋白拷贝数一致	链 D； UniProt 1–697	片段：Motor Domain	MG MAGNESIUM ION × 1 VO4 VANADATE ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION, HANGING DROP；pH 7.2；289 K；11% PEG 8K, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 289K	分辨率 3.00 Å R-free 0.273

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 1LKX	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
4A7F Structure of the Actin-Tropomyosin-Myosin Complex (rigor ATM 3) 提交 2011-11-14	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验方法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 × 10 PDB 声明：decameric	链 C 1–697（697 aa）片段：RESIDUES 1-697 链 G 1–697（697 aa）片段：RESIDUES 1-697 链 J 1–697（697 aa）片段：RESIDUES 1-697	突变：YES 突变：YES 突变：YES	ADP ADENOSINE-5'-DIPHOSPHATE × 5 CA CALCIUM ION × 5	ELECTRON MICROSCOPY cryo-EM缓冲液 5 MM HEPES-OH, 100 MM KCL, 2 MM MGCL2, 50 MM GLUTAMINE, 50 MM ARGININE；pH 7.2；5 MM HEPES-OH, 100 MM KCL, 2 MM MGCL2, 50 MM GLUTAMINE, 50 MM ARGININE cryo-EM玻璃化条件冷冻剂 ETHANE；LIQUID ETHANE	分辨率 7.70 Å
4A7H Structure of the Actin-Tropomyosin-Myosin Complex (rigor ATM 2) 提交 2011-11-14	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验方法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 × 10 PDB 声明：decameric	链 C 1–697（697 aa）片段：RESIDUES 1-697 链 I 1–697（697 aa）片段：RESIDUES 1-697 链 J 1–697（697 aa）片段：RESIDUES 1-697	突变：YES 突变：YES 突变：YES	ADP ADENOSINE-5'-DIPHOSPHATE × 5 CA CALCIUM ION × 5	ELECTRON MICROSCOPY cryo-EM缓冲液 5MM TRIS, 100MM KCL, 2MM MGCL2, 50MM GLUTAMINE, 50MM ARGININ；pH 7.2；5MM TRIS, 100MM KCL, 2MM MGCL2, 50MM GLUTAMINE, 50MM ARGININ cryo-EM玻璃化条件冷冻剂 ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 90, TEMPERATURE- 101, INSTRUMENT- GATAN CRYOPLUNGE 3, METHOD- MANUAL BLOTTING FOR APPROXIMATELY 15 SECONDS,	分辨率 7.80 Å
4A7L Structure of the Actin-Tropomyosin-Myosin Complex (rigor ATM 1) 提交 2011-11-14	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验方法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 × 10 PDB 声明：decameric	链 C 1–697（697 aa）片段：RESIDUES 1-697 链 G 1–697（697 aa）片段：RESIDUES 1-697 链 J 1–697（697 aa）片段：RESIDUES 1-697	突变：YES 突变：YES 突变：YES	ADP ADENOSINE-5'-DIPHOSPHATE × 5 CA CALCIUM ION × 5	ELECTRON MICROSCOPY cryo-EM缓冲液 5MM TRIS, 100MM KCL, 2MM MGCL2, 50MM GLUTAMINE, 50MM ARGININ；pH 7.2；5MM TRIS, 100MM KCL, 2MM MGCL2, 50MM GLUTAMINE, 50MM ARGININ cryo-EM玻璃化条件冷冻剂 ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 90, TEMPERATURE- 101, INSTRUMENT- GATAN CRYOPLUNGE 3, METHOD- MANUAL BLOTTING FOR APPROXIMATELY 15 SECONDS,	分辨率 8.10 Å

共 3 个其他 PDB 条目、3 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	MYOE_DICDI
Isoform	—
PDB实体	1
链与序列区间	作者链 A； PDB构建体 1–697； UniProt 1–697 作者链 B； PDB构建体 1–697； UniProt 1–697 作者链 C； PDB构建体 1–697； UniProt 1–697 作者链 D； PDB构建体 1–697； UniProt 1–697

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	1lkx
沉积日期 deposition_date	2002-04-26
结构标题 title	MOTOR DOMAIN OF MYOE, A CLASS-I MYOSIN
关键词 keywords	MYOSIN MOTOR DOMAIN, LEVER ARM, CONVERTER DOMAIN, CONTRACTILE PROTEIN; CONTRACTILE PROTEIN
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	58.17 Å
回转半径 Rg (电子) rg_electron	58.73 Å
零角强度 I(0) i0	1321720000.00
分子量 molecular_weight	302150.0 kDa
排除体积 excluded_volume	377580 Å³
包络体积 envelope_volume	541770 Å³
水化壳体积 shell_volume	81925 Å³
包络直径 envelope_diameter	220.5 Å
壳层 Rg shell_rg	55.46 Å
包络 Rg envelope_rg	57.57 Å
形状 Rg shape_rg	58.73 Å
总 Rg total_rg	58.63 Å
总原子数 total_atoms	21201
残基数 n_residues	2639
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	197.2 Å
Rg (实空间) rg_real	58.74 Å
Rg 误差 (实空间) rg_real_error	1.88 Å
I(0) (实空间) i0_real	1.3220e+09
I(0) 误差 (实空间) i0_real_error	2.4640e+07
Rg (倒空间) rg_reciprocal	57.67 Å
I(0) (倒空间) i0_reciprocal	1319000000.0000
解质量估计 total_estimate	0.8139
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	65.7 Å
偏度 Skewness skewness	0.593
峰度 Kurtosis kurtosis	-0.049
角度范围 angular_range	— – 0.1350 Å⁻¹
当前正则化参数 α current_alpha	0.0003
最高正则化参数 α highest_alpha	50860000.0000
实空间数据点数 n_real_points	28
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.826; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.899; Smooth: 0.201

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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)

实体 1 Entity 1 polymer

描述 description	MYOSIN IE HEAVY CHAIN
分子量 formula_weight	79165.3 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	A,B,C,D
原子数 atom_count	21265

MIPKTKAEGVPDFVLLNQITENAFIENLTMRHKSDNIYTYIGDVVISTNPFKNLNIYKESDIKAYNGRYKYEMPPHMYALANDAYRSMRQSQENQCVIISGESGAGKTEASKKIMQFLTFVSSNQSPNGERISKMLLDSNPLLEAFGNAKTLRNDNSSRFGKYMEMQFNAVGSPIGGKITNYLLEKSRVVGRTQGERSFHIFYQMLKGLSQSKLDELGLTPNAPAYEYLKKSGCFDVSTIDDSGEFKIIVKAMETLGLKESDQNSIWRILAAILHIGNITFAEAAEQRTGTTTVKVSDTKSLAAAASCLKTDQQSLSIALCYRSISTGVGKRCSVISVPMDCNQAAYSRDALAKALYERLFNWLVSKINTIINCTTEKGPVIGILDIYGFEVFQNNSFEQLNINFCNEKLQQLFIELTLKSEQEEYVREGIEWKNIEYFNNKPICELIEKKPIGLISLLDEACLIAKSTDQTFLDSICKQFEKNPHLQSYVVSKDRSIGDTCFRLKHYAGDVTYDVRGFLDKNKDTLFGDLISSMQSSSDPLVQGLFPPTRPEDSKKRPETAGSQFRNAMNALITTLLACSPHYVRCIKSNDNKQAGVIDEDRVRHQVRYLGLLENVRVRRAGFAGRIEYTRFYNRYKMLCKKTWPSFNGTAKQATELILQQHNIDKEEIRMGKTKVFIRNPTTLFYFEEKRELEMP

来源 Source

来源生物 organism	Dictyostelium discoideum
NCBI 分类编号 ncbi_taxonomy_id	44689
宿主生物 host_organism	Dictyostelium discoideum

实体 2 Entity 2 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

实体 3 Entity 3 non-polymer

描述 description	VANADATE ION
分子量 formula_weight	114.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

实体 4 Entity 4 non-polymer

描述 description	ADENOSINE-5'-DIPHOSPHATE
分子量 formula_weight	427.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

实体 5 Entity 5 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	64

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7. 折叠分类 (SCOP + CATH) 20 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1lkxa_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family family	c.37.1.9 — Motor proteins

结构域编号 domain_id	d1lkxb_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family family	c.37.1.9 — Motor proteins

结构域编号 domain_id	d1lkxc_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family family	c.37.1.9 — Motor proteins

结构域编号 domain_id	d1lkxd_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family family	c.37.1.9 — Motor proteins

CATH v4.4 (16 domains)

结构域编号 domain_id	1lkxA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	850 — Kinesin
同源超家族 H-superfamily homologous superfamily	10 — Kinesin motor domain

结构域编号 domain_id	1lkxA02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	10 — Arc Repressor Mutant, subunit A
同源超家族 H-superfamily homologous superfamily	820 —

结构域编号 domain_id	1lkxA03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
同源超家族 H-superfamily homologous superfamily	720 — Myosin VI head, motor domain, U50 subdomain

结构域编号 domain_id	1lkxA04
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
同源超家族 H-superfamily homologous superfamily	530 —

结构域编号 domain_id	1lkxB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	850 — Kinesin
同源超家族 H-superfamily homologous superfamily	10 — Kinesin motor domain

结构域编号 domain_id	1lkxB02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	10 — Arc Repressor Mutant, subunit A
同源超家族 H-superfamily homologous superfamily	820 —

结构域编号 domain_id	1lkxB03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
同源超家族 H-superfamily homologous superfamily	720 — Myosin VI head, motor domain, U50 subdomain

结构域编号 domain_id	1lkxB04
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
同源超家族 H-superfamily homologous superfamily	530 —

结构域编号 domain_id	1lkxC01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	850 — Kinesin
同源超家族 H-superfamily homologous superfamily	10 — Kinesin motor domain

结构域编号 domain_id	1lkxC02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	10 — Arc Repressor Mutant, subunit A
同源超家族 H-superfamily homologous superfamily	820 —

结构域编号 domain_id	1lkxC03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
同源超家族 H-superfamily homologous superfamily	720 — Myosin VI head, motor domain, U50 subdomain

结构域编号 domain_id	1lkxC04
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
同源超家族 H-superfamily homologous superfamily	530 —

结构域编号 domain_id	1lkxD01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	850 — Kinesin
同源超家族 H-superfamily homologous superfamily	10 — Kinesin motor domain

结构域编号 domain_id	1lkxD02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	10 — Arc Repressor Mutant, subunit A
同源超家族 H-superfamily homologous superfamily	820 —

结构域编号 domain_id	1lkxD03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
同源超家族 H-superfamily homologous superfamily	720 — Myosin VI head, motor domain, U50 subdomain

结构域编号 domain_id	1lkxD04
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
同源超家族 H-superfamily homologous superfamily	530 —

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8. 引用文献 (1)

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晶胞边长 a length_a	51.818 Å
晶胞边长 b length_b	143.667 Å
晶胞边长 c length_c	236.050 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	94.86 °
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	3.000 Å
最低分辨率 resolution_low	50.000 Å
R 因子 r_factor	—
R_work r_work	0.2280
R_free r_free	0.2730

fit	/app/data/saxs_computation/lk/1lkx/1lkx.fit
pddf	/app/data/pr_computation/lk/1lkx/1lkx.pr.out
profile	/app/data/saxs_computation/lk/1lkx/1lkx.dat