1s3s

Crystal structure of AAA ATPase p97/VCP ND1 in complex with p47 C

Method: X-RAY DIFFRACTION

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

;Transitional endoplasmic reticulum ATPase (TER ATPase) (15S Mg(2+)- ATPase p97 subunit) (Valosin containing protein) (VCP) [Contains: Valosin] ;

Mus musculus

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	蛋白异源复合物	异源复合物	蛋白 9	p47 protein × 3 （O35987） ADENOSINE-5'-DIPHOSPHATE × 6 water × 9	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	TERA_MOUSE
Isoform	—
PDB实体	1
链与序列区间	作者链 A； PDB构建体 1–458； UniProt 1–457 作者链 B； PDB构建体 1–458； UniProt 1–457 作者链 C； PDB构建体 1–458； UniProt 1–457 作者链 D； PDB构建体 1–458； UniProt 1–457 作者链 E； PDB构建体 1–458； UniProt 1–457 作者链 F； PDB构建体 1–458； UniProt 1–457

p47 protein

Rattus norvegicus

UniProt O35987

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	蛋白异源复合物	异源复合物	蛋白 9	;Transitional endoplasmic reticulum ATPase (TER ATPase) (15S Mg(2+)- ATPase p97 subunit) (Valosin containing protein) (VCP) [Contains: Valosin] ; × 6 （Q01853） ADENOSINE-5'-DIPHOSPHATE × 6 water × 9	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	NSF1C_RAT
Isoform	—
PDB实体	2
链与序列区间	作者链 G； PDB构建体 1–127； UniProt 244–370 作者链 H； PDB构建体 1–127； UniProt 244–370 作者链 I； PDB构建体 1–127； UniProt 244–370

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	1s3s
沉积日期 deposition_date	2004-01-14
结构标题 title	Crystal structure of AAA ATPase p97/VCP ND1 in complex with p47 C
关键词 keywords	AAA ATPase, p97, p47, protein-protein complex, UBX domain, PROTEIN BINDING; PROTEIN BINDING
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。

1s3s__assembly_1__model_1

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

下载该曲线 .dat

1s3s__assembly_1__model_1 | I(q)

100 个绘图点；横轴和纵轴均采用对数尺度。

1s3s__assembly_1__model_1 | P(r) · Pending

P(r) 将按相同 assembly/model 分别计算和展示。

Rg（Guinier）	55.78 Å
Rg（电子密度）	55.93 Å
总 Rg	55.89 Å
原子数	22304
残基数	2871
排除体积	396990 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	`1s3s__assembly_1__model_1`	nonameric （9）	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 (4)

实体 1 Entity 1 polymer

描述 description	;Transitional endoplasmic reticulum ATPase (TER ATPase) (15S Mg(2+)- ATPase p97 subunit) (Valosin containing protein) (VCP) [Contains: Valosin] ;
分子量 formula_weight	51027.5 kDa
来源方法 src_method	man
拷贝数 entity_count	6

聚合物 Polymer

聚合物类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F
原子数 atom_count	22367

MASGADSKGDDLSTAILKQKNRPNRLIVDEAINEDNSVVSLSQPKMDELQLFRGDTVLLKGKKRREAVCIVLSDDTCSDEKIRMNRVVRNNLRVRLGDVISIQPCPDVKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVETDPSPYCIVAPDTVIHCEGEPIKREDEEESLNEVGYDDVGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHGHVGADLAALCSEAALQAIRKKMDLIDLEDETIDAEVMNSLAVTMDDFRWALSQ

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI 分类编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

实体 2 Entity 2 polymer

描述 description	p47 protein
分子量 formula_weight	13775.6 kDa
来源方法 src_method	man
拷贝数 entity_count	3

聚合物 Polymer

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

VKPKGAFKAFTGEGQKLGSTAPQVLNTSSPAQQAENEAKASSSILINEAEPTTNIQIRLADGGRLVQKFNHSHRISDIRLFIVDARPAMAATSFVLMTTFPNKELADENQTLKEANLLNAVIVQRLT

来源 Source

来源生物 organism	Rattus norvegicus
通用名 common_name	Norway rat
NCBI 分类编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Escherichia coli

实体 3 Entity 3 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	6

实体 4 Entity 4 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	63

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6. 折叠分类 (SCOP + CATH) 47 domains

SCOP 2.08 (21 domains)

结构域编号 domain_id	d1s3sa1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.52 — Double psi beta-barrel
超家族 Superfamily superfamily	b.52.2 — ADC-like
家族 Family family	b.52.2.3 — Cdc48 N-terminal domain-like

结构域编号 domain_id	d1s3sa2
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.37.1.20 — Extended AAA-ATPase domain

结构域编号 domain_id	d1s3sa3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.31 — Cdc48 domain 2-like
超家族 Superfamily superfamily	d.31.1 — Cdc48 domain 2-like
家族 Family family	d.31.1.1 — Cdc48 domain 2-like

结构域编号 domain_id	d1s3sb1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.52 — Double psi beta-barrel
超家族 Superfamily superfamily	b.52.2 — ADC-like
家族 Family family	b.52.2.3 — Cdc48 N-terminal domain-like

结构域编号 domain_id	d1s3sb2
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.37.1.20 — Extended AAA-ATPase domain

结构域编号 domain_id	d1s3sb3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.31 — Cdc48 domain 2-like
超家族 Superfamily superfamily	d.31.1 — Cdc48 domain 2-like
家族 Family family	d.31.1.1 — Cdc48 domain 2-like

结构域编号 domain_id	d1s3sc1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.52 — Double psi beta-barrel
超家族 Superfamily superfamily	b.52.2 — ADC-like
家族 Family family	b.52.2.3 — Cdc48 N-terminal domain-like

结构域编号 domain_id	d1s3sc2
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.37.1.20 — Extended AAA-ATPase domain

结构域编号 domain_id	d1s3sc3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.31 — Cdc48 domain 2-like
超家族 Superfamily superfamily	d.31.1 — Cdc48 domain 2-like
家族 Family family	d.31.1.1 — Cdc48 domain 2-like

结构域编号 domain_id	d1s3sd1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.52 — Double psi beta-barrel
超家族 Superfamily superfamily	b.52.2 — ADC-like
家族 Family family	b.52.2.3 — Cdc48 N-terminal domain-like

结构域编号 domain_id	d1s3sd2
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.37.1.20 — Extended AAA-ATPase domain

结构域编号 domain_id	d1s3sd3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.31 — Cdc48 domain 2-like
超家族 Superfamily superfamily	d.31.1 — Cdc48 domain 2-like
家族 Family family	d.31.1.1 — Cdc48 domain 2-like

结构域编号 domain_id	d1s3se1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.52 — Double psi beta-barrel
超家族 Superfamily superfamily	b.52.2 — ADC-like
家族 Family family	b.52.2.3 — Cdc48 N-terminal domain-like

结构域编号 domain_id	d1s3se2
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.37.1.20 — Extended AAA-ATPase domain

结构域编号 domain_id	d1s3se3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.31 — Cdc48 domain 2-like
超家族 Superfamily superfamily	d.31.1 — Cdc48 domain 2-like
家族 Family family	d.31.1.1 — Cdc48 domain 2-like

结构域编号 domain_id	d1s3sf1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.52 — Double psi beta-barrel
超家族 Superfamily superfamily	b.52.2 — ADC-like
家族 Family family	b.52.2.3 — Cdc48 N-terminal domain-like

结构域编号 domain_id	d1s3sf2
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.37.1.20 — Extended AAA-ATPase domain

结构域编号 domain_id	d1s3sf3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.31 — Cdc48 domain 2-like
超家族 Superfamily superfamily	d.31.1 — Cdc48 domain 2-like
家族 Family family	d.31.1.1 — Cdc48 domain 2-like

结构域编号 domain_id	d1s3sg_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.15 — beta-Grasp (ubiquitin-like)
超家族 Superfamily superfamily	d.15.1 — Ubiquitin-like
家族 Family family	d.15.1.2 — UBX domain

结构域编号 domain_id	d1s3sh_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.15 — beta-Grasp (ubiquitin-like)
超家族 Superfamily superfamily	d.15.1 — Ubiquitin-like
家族 Family family	d.15.1.2 — UBX domain

结构域编号 domain_id	d1s3si_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.15 — beta-Grasp (ubiquitin-like)
超家族 Superfamily superfamily	d.15.1 — Ubiquitin-like
家族 Family family	d.15.1.2 — UBX domain

CATH v4.4 (26 domains)

结构域编号 domain_id	1s3sA01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	40 — Barwin-like endoglucanases
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	1s3sA02
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	1s3sA03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	330 — Vcp-like ATPase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1s3sA04
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	60 —

结构域编号 domain_id	1s3sB01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	40 — Barwin-like endoglucanases
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	1s3sB02
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	1s3sB03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	330 — Vcp-like ATPase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1s3sB04
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	60 —

结构域编号 domain_id	1s3sC01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	40 — Barwin-like endoglucanases
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	1s3sC02
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	1s3sC03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	330 — Vcp-like ATPase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1s3sC04
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	60 —

结构域编号 domain_id	1s3sD01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	40 — Barwin-like endoglucanases
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	1s3sD02
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	1s3sD03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	330 — Vcp-like ATPase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1s3sD04
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	60 —

结构域编号 domain_id	1s3sE01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	40 — Barwin-like endoglucanases
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	1s3sE02
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	1s3sE03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	330 — Vcp-like ATPase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1s3sE04
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	60 —

结构域编号 domain_id	1s3sF01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	40 — Barwin-like endoglucanases
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	1s3sF02
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	1s3sF03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	330 — Vcp-like ATPase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1s3sF04
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	60 —

结构域编号 domain_id	1s3sG00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	20 — Ubiquitin-like (UB roll)
同源超家族 H-superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

结构域编号 domain_id	1s3sH00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	20 — Ubiquitin-like (UB roll)
同源超家族 H-superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

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晶胞边长 a length_a	157.719 Å
晶胞边长 b length_b	157.719 Å
晶胞边长 c length_c	243.195 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	36

空间群 space_group	P 65
空间群编号 int_tables_number	170
晶系 crystal_system	—

分辨率 resolution	2.900 Å
最低分辨率 resolution_low	39.700 Å
R 因子 r_factor	—
R_work r_work	0.2480
R_free r_free	0.2940

Crystal structure of AAA ATPase p97/VCP ND1 in complex with p47 C

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

;Transitional endoplasmic reticulum ATPase (TER ATPase) (15S Mg(2+)- ATPase p97 subunit) (Valosin containing protein) (VCP) [Contains: Valosin] ;

当前结构中的状态

数据库中的同蛋白其他状态

p47 protein

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

1s3s__assembly_1__model_1

1s3s__assembly_1__model_1 | I(q)

1s3s__assembly_1__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 (4)

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 non-polymer

实体 4 Entity 4 water

6. 折叠分类 (SCOP + CATH) 47 domains

SCOP 2.08 (21 domains)

CATH v4.4 (26 domains)

7. 引用文献 (1)

Crystal structure of AAA ATPase p97/VCP ND1 in complex with p47 C

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

;Transitional endoplasmic reticulum ATPase (TER ATPase) (15S Mg(2+)- ATPase p97 subunit) (Valosin containing protein) (VCP) [Contains: Valosin] ;

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

p47 protein

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

1s3s__assembly_1__model_1

1s3s__assembly_1__model_1 | I(q)

1s3s__assembly_1__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 (4)

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 non-polymer

实体 4 Entity 4 water

6. 折叠分类 (SCOP + CATH) 47 domains

SCOP 2.08 (21 domains)

CATH v4.4 (26 domains)

7. 引用文献 (1)