3vkg

X-ray structure of an MTBD truncation mutant of dynein motor domain

Method: X-RAY DIFFRACTION

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

Dynein heavy chain, cytoplasmic

Dictyostelium discoideum

当前结构中的状态

Assembly	物理组成	蛋白状态	分子拷贝数	共同组分	数据核对
1	蛋白同源多聚体	同源多聚体	蛋白 2	ADENOSINE-5'-DIPHOSPHATE × 8 SPERMINE × 4 MAGNESIUM ION × 3 water × 2	与蛋白数一致
2	蛋白单体	单体	蛋白 1	ADENOSINE-5'-DIPHOSPHATE × 4 SPERMINE × 2 MAGNESIUM ION × 1 water × 1	与蛋白数一致
3	蛋白单体	单体	蛋白 1	ADENOSINE-5'-DIPHOSPHATE × 4 SPERMINE × 2 MAGNESIUM ION × 2 water × 1	与蛋白数一致

数据库中的同蛋白其他状态

查看构建体与数据证据

UniProt名称	DYHC_DICDI
Isoform	—
PDB实体	1
链与序列区间	作者链 A； PDB构建体 25–2008； UniProt 1388–3371 作者链 A； PDB构建体 2011–3245； UniProt 3496–4730 作者链 B； PDB构建体 25–2008； UniProt 1388–3371 作者链 B； PDB构建体 2011–3245； UniProt 3496–4730

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	3vkg
沉积日期 deposition_date	2011-11-16
结构标题 title	X-ray structure of an MTBD truncation mutant of dynein motor domain
关键词 keywords	AAA+ protein, molecular motor, microtubles, motor protein; MOTOR PROTEIN
实验方法 method	X-RAY DIFFRACTION

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3. Official assembly/model 理论 SAXS Official SAXS Profiles

页面只读取最新 assembly 计算结果。每一条曲线都对应明确的 PDB、official biological assembly 和 coordinate model。

3vkg__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

下载该曲线 .dat

3vkg__assembly_3__model_1 | I(q)

100 个绘图点；横轴和纵轴均采用对数尺度。

3vkg__assembly_3__model_1 | P(r) · Pending

P(r) 将按相同 assembly/model 分别计算和展示。

Rg（Guinier）	52.88 Å
Rg（电子密度）	53.09 Å
总 Rg	53.16 Å
原子数	22284
残基数	2853
排除体积	396670 Å³
最大 q	0.500 Å⁻¹

Assembly	Model	结构单元	聚集说明	状态	CRYSOL	操作
1	1	`3vkg__assembly_1__model_1`	dimeric （2）	成功	4.1.3-1-20251215 (887e7ef)	查看下载
2	1	`3vkg__assembly_2__model_1`	monomeric （1）	成功	4.1.3-1-20251215 (887e7ef)	查看下载
3	1	`3vkg__assembly_3__model_1`	monomeric （1）	成功	4.1.3-1-20251215 (887e7ef)	查看下载

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4. 晶体学与实验 4. Crystallography & Experiment

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5. 实体与聚合物信息 Entities & Polymers (5)

实体 1 Entity 1 polymer

描述 description	Dynein heavy chain, cytoplasmic
分子量 formula_weight	370426.7 kDa
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	45284

MTRHHHHHHGGGDYKDDDDKGGGKVPVEEEIQDLKAVWVELSNTWQEIDSLKETAWSAIIPRKVRKSLEDTLQKLKNLPNRIRQYSAFDHAQNLIKIYLKGNAIITDLHSEAIKDRHWKILKKRLNTNWIITELTLGSIWDSDLARNENIYREVITAAQGEIALEEFLKGVREFWTTLELDLVNYQRKCKLVRGWDDLFNKLAEHLNSISAMKMSPYYKVFEEEANHWDDRLNKVRSLLDVWIDVQRRWVYLEGIFSGSGDINQLLPAESTRFKSINSEFIAILKKVSGAPLILEVLAIERIQQTMERLSDLLGKVQKALGEYLERQRSAFARFYFVGDEDLLEIIGNSKDIIKIQKHFRKMFAGLANLTLDDEKTTIIGMSSAEGETVTFKKPISIANGPKIHEWLTMVESEMKSTLATLLSESLQHFNQVDVNDHSKYSEWVDNYPTQLVLLTSQIVWSTQVDQALGGGTLQQSKIQEQLQSIEQTTQMILNNLADSVLQDLSAQKRKKFEHLITELVHQRDVVRQLQKCKNLTGNKDFDWLYHMRYYYDATQENVLHKLVIHMANATFYYGFEYLGIGERLVQTPLTDRCYLTLTQALESRMGGNPFGPAGTGKTETVKALGSQLGRFVLVFCCDEGFDLQAMSRIFVGLCQCGAWGCFDEFNRLEERILSAVSQQIQTIQVALKENSKEVELLGGKNISLHQDMGIFVTMNPGYAGRSNLPDNLKKLFRSMAMIKPDREMIAQVMLYSQGFKTAEVLAGKIVPLFKLCQEQLSAQSHYDFGLRALKSVLVSAGGIKRKCQPPQLPPITDAESKTKADQIYCQYEIGVLLNSINDTMIPKLVADDIPLIQSLLLDVFPGSQLQPIQMDQLRKKIQEIAKQRHLVTKQEWVEKILQLHQILNINHGVMMVGPSGGGKTTSWEVYLEAIEQVDNIKSEAHVMDPKAITKDQLFGSLDLTTREWTDGLFTATLRRIIDNVRGESTKRHWIIFDGDVDPEWVENLNSLLDDNKLLTLPNGERLALPNNVRVMFEVQDLKYATLATISRCGMVWFSEEILTTQMIFQNYLDTLSNEPFDPQEKEQQKRNENAQLQQQQQTTITSPILTSPPTTSSSSRSTTSTTSMIPAGLKVQKECAAIISQYFEPGGLVHKVLEDAGQRPHIMDFTRLRVLNSFFSLMNRSIVNVIEYNQLHSDFPMSPENQSNYITNRLLYSLMWGLGGSMGLVERENFSKFIQTIAITPVPANTIPLLDYSVSIDDANWSLWKNKVPSVEVETHKVASPDVVIPTVDTTRHVDVLHAWLSEHRPLILCGPPGSGKTMTLTSTLRAFPDFEVVSLNFSSATTPELLLKTFDHHCEYKRTPSGETVLRPTQLGKWLVVFCDEINLPSTDKYGTQRVITFIRQMVEKGGFWRTSDHTWIKLDKIQFVGACNPPTDAGRVQLTHRFLRHAPILLVDFPSTSSLTQIYGTFNRALMKLLPNLRSFADNLTDAMVEFYSESQKRFTPDIQAHYIYSPRELSRWDRALLEAIQTMDGCTLEGLVRLWAHEALRLFQDRLVETEEKEWTDKKIDEVALKHFPSVNLDALKRPILYSNWLTKDYQPVNRSDLREYVKARLKVFYEEELDVPLVLFNEVLDHILRIDRVFRQPQGHALLIGVSGGGKSVLSRFVAWMNGLSIYTIKVNNNYKSSDFDDDLRMLLKRAGCKEEKICFIFDESNVLESSFLERMNTLLAGGEVPGLFEGEEFTALMHACKETAQRNGLILDSEEELYKYFTSQVRRNLHVVFTMNPASPDFHNRSATSPALFNRCVLDWFGEWSPEALFQVGSEFTRNLDLENPQYIAPPVFIQEAEIMGNNLMAIPPSHRDAVVSSLVYIHQTIGEANIRLLKRQGRQNYVTPRHYLDFINQVVLLINEKRDQLEEEQLHLNIGLKKLRDTEAQVKDLQVSLAQKNRELDVKNEQANQKLKQMVQDQQAAEIKQKDARELQVQLDVRNKEIAVQKVKAYADLEKAEPTGPLREEVEQLENAANELKLKQDEIVATITALEKSIATYKEEYATLIRETEQIKTESSKVKNKVDRSIALLDNLNSERGRWEQQSENFNTQMSTVVGDVVLASAFLAYIGFFDQNFRTDLMRKWMIRLDSVGIKFKSDLSVPSFLSKPEERLNWHANSLPSDELCIENAIMLKRFNRYPLVIDPSGQAMEFLMNQYADKKITKTSFLDSSFMKNLESALRFGCPLLVQDVENIDPVLNPVLNKEIRKKGGRILIRLGDQDVDFSPSFMIFLFTRDPTAHFTPDLCSRVTFVNFTVTPSSLQSQCLHEALKTERPDTHKKRSDLLKIQGEFQVKLRILEKSLLNALSQASGNILDDDSVISTLETLKKETTEIALKVEETETVMQEISEVSALYNPMALSCSRVYFAMEELSQFHLYQFSLRAFLDIFYNLLNNNPNLVDKKDPNERLVYLSKDIFSMTFNRVTRTLLNDDKLTFALQLTIISVKGTSNEIEESEWDFLLKGGDNLTSIKETIPQLDSLLSTTQQKWLICLRQQVPSFSKLVDHIQQNSSDWKQFFGKDQVGEPIIPESWIVAQAQLSNQQSTIVSNFRKILLMKAFHSDRVLQYSHSFVCSVFGEDFLNTQELDMANIVEKEVKSSSPLLLCSVPGYDASSKVDDLALQLHKQYKSFAIGSPEGFELAEKSIYAAAKSGTWVLLKNIHLAPQWLVQLEKKLHSLSPHPSFRLFMTSEIHPALPANLLRMSNVFSYENPPGVKANLLHTFIGIPATRMDKQPAERSRIYFLLAWFHAIIQERLRYIPLGWTKFFEFNDADLRGALDSIDYWVDLYSKGRSNIDPDKIPWIAVRTILGSTIYGGRIDNEFDMRLLYSFLEQLFTPSAFNPDFPLVPSIGLSVPEGTTRAHFMKWIEALPEISTPIWLGLPENAESLLLSNKARKMINDLQKMQSSEEDGEDDQVSGSSKKESSSSSSEDKGKAKLRATITEWTKLLPKPLKQLKRTTQNIKDPLFRCFEREISTGGKLVKKITNDLANLLELISGNIKSTNYLRSLTTSISKGIVPKEWKWYSVPETISLSVWISDFSKRMQQLSEISESSDYSSIQVWLGGLLNPEAYITATRQSASQLNGWSLENLRLHASSLGKISSEGGASFNVKGMALEGAVWNNDQLTPTDILSTPISIATLTWKDKDDPIFNNSSSKLSVPVYLNETRSELLFSIDLPYDQSTSKQNWYQRSVSISSWKSDI

来源 Source

来源生物 organism	Dictyostelium discoideum
通用名 common_name	Slime mold
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	ADENOSINE-5'-DIPHOSPHATE
分子量 formula_weight	427.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	8

实体 3 Entity 3 non-polymer

描述 description	SPERMINE
分子量 formula_weight	202.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

实体 4 Entity 4 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	3

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	42

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6. 折叠分类 (SCOP + CATH) 25 domains

CATH v4.4 (25 domains)

结构域编号 domain_id	3vkgA02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
同源超家族 H-superfamily homologous superfamily	100 — Dynein motor heavy chain, linker domain, N-terminal subdomain

结构域编号 domain_id	3vkgA03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	180 — Split barrel-like
同源超家族 H-superfamily homologous superfamily	20 — Dynein motor heavy chain, linker domain, subdomain 3

结构域编号 domain_id	3vkgA04
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	1120 — Dynein motor heavy chain, linker domain, subdomain 4

结构域编号 domain_id	3vkgA05
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

结构域编号 domain_id	3vkgA06
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	710 — Dynein motor, AAA1 domain, small subdomain

结构域编号 domain_id	3vkgA07
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

结构域编号 domain_id	3vkgA08
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	472 — Cyclin A; domain 1
同源超家族 H-superfamily homologous superfamily	130 — Dynein motor, AAA2 domain, small subdomain

结构域编号 domain_id	3vkgA09
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	920 — Histone Acetyltransferase; Chain A
同源超家族 H-superfamily homologous superfamily	30 —

结构域编号 domain_id	3vkgA10
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

结构域编号 domain_id	3vkgA11
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	920 — Histone Acetyltransferase; Chain A
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	3vkgA12
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	287 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily	2610 —

结构域编号 domain_id	3vkgA13
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

结构域编号 domain_id	3vkgA14
类 Class class	6 — Special
架构 Architecture architecture	10 — Helix non-globular
拓扑 Topology topology	140 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily	1060 —

结构域编号 domain_id	3vkgA15
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	1220 —

结构域编号 domain_id	3vkgA17
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

结构域编号 domain_id	3vkgA18
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	720 — Region D6 of dynein motor

结构域编号 domain_id	3vkgA20
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	490 — Hypothetical upf0131 protein ytfp
同源超家族 H-superfamily homologous superfamily	20 — Dynein motor C sequence, barrel region

结构域编号 domain_id	3vkgB01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
同源超家族 H-superfamily homologous superfamily	100 — Dynein motor heavy chain, linker domain, N-terminal subdomain

结构域编号 domain_id	3vkgB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	180 — Split barrel-like
同源超家族 H-superfamily homologous superfamily	20 — Dynein motor heavy chain, linker domain, subdomain 3

结构域编号 domain_id	3vkgB03
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	1120 — Dynein motor heavy chain, linker domain, subdomain 4

结构域编号 domain_id	3vkgB04
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	710 — Dynein motor, AAA1 domain, small subdomain

结构域编号 domain_id	3vkgB05
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

结构域编号 domain_id	3vkgB06
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	920 — Histone Acetyltransferase; Chain A
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	3vkgB07
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	720 — Region D6 of dynein motor

结构域编号 domain_id	3vkgB08
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	490 — Hypothetical upf0131 protein ytfp
同源超家族 H-superfamily homologous superfamily	20 — Dynein motor C sequence, barrel region

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晶胞边长 a length_a	204.256 Å
晶胞边长 b length_b	221.806 Å
晶胞边长 c length_c	192.898 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	90.00 °
晶胞分子数 Z z_pdb	8

空间群 space_group	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	2.810 Å
最低分辨率 resolution_low	96.450 Å
R 因子 r_factor	0.2620
R_work r_work	0.2620
R_free r_free	0.3190

X-ray structure of an MTBD truncation mutant of dynein motor domain

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

Dynein heavy chain, cytoplasmic

当前结构中的状态

数据库中的同蛋白其他状态

2. 结构基本信息 2. Structure Basics

3. Official assembly/model 理论 SAXS Official SAXS Profiles

3vkg__assembly_3__model_1

3vkg__assembly_3__model_1 | I(q)

3vkg__assembly_3__model_1 | P(r) · Pending

4. 晶体学与实验 4. Crystallography & Experiment

晶胞参数 Unit Cell

对称性 Symmetry

精修参数 Refinement

衍射实验 Diffraction

5. 实体与聚合物信息 Entities & Polymers (5)

实体 1 Entity 1 polymer

聚合物 Polymer

来源 Source

实体 2 Entity 2 non-polymer

实体 3 Entity 3 non-polymer

实体 4 Entity 4 non-polymer

实体 5 Entity 5 water

6. 折叠分类 (SCOP + CATH) 25 domains

CATH v4.4 (25 domains)

7. 引用文献 (1)

X-ray structure of an MTBD truncation mutant of dynein motor domain

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

Dynein heavy chain, cytoplasmic

当前结构中的状态

数据库中的同蛋白其他状态

单体

同源二聚体

同源四聚体

其他同源多聚体

异源或核酸复合物

2. 结构基本信息 2. Structure Basics

3. Official assembly/model 理论 SAXS Official SAXS Profiles

3vkg__assembly_3__model_1

3vkg__assembly_3__model_1 | I(q)

3vkg__assembly_3__model_1 | P(r) · Pending

4. 晶体学与实验 4. Crystallography & Experiment

晶胞参数 Unit Cell

对称性 Symmetry

精修参数 Refinement

衍射实验 Diffraction

5. 实体与聚合物信息 Entities & Polymers (5)

实体 1 Entity 1 polymer

聚合物 Polymer

来源 Source

实体 2 Entity 2 non-polymer

实体 3 Entity 3 non-polymer

实体 4 Entity 4 non-polymer

实体 5 Entity 5 water

6. 折叠分类 (SCOP + CATH) 25 domains

CATH v4.4 (25 domains)

7. 引用文献 (1)