1cd3

PROCAPSID OF BACTERIOPHAGE PHIX174

Method: X-RAY DIFFRACTION
▼

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

PROTEIN (SCAFFOLDING PROTEIN GPD)

物种未注明

UniProt P69486

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 420 PROTEIN (CAPSID PROTEIN GPF) × 60 (P03641) PROTEIN (SPIKE PROTEIN GPG) × 60 (P03643) PROTEIN (SCAFFOLDING PROTEIN GPB) × 60 (P03633) water × 420 与蛋白数一致
2 蛋白异源复合物 异源复合物 蛋白 7 PROTEIN (CAPSID PROTEIN GPF) × 1 (P03641) PROTEIN (SPIKE PROTEIN GPG) × 1 (P03643) PROTEIN (SCAFFOLDING PROTEIN GPB) × 1 (P03633) water × 7 与蛋白数一致
3 蛋白异源复合物 异源复合物 蛋白 35 PROTEIN (CAPSID PROTEIN GPF) × 5 (P03641) PROTEIN (SPIKE PROTEIN GPG) × 5 (P03643) PROTEIN (SCAFFOLDING PROTEIN GPB) × 5 (P03633) water × 35 与蛋白数一致
4 蛋白异源复合物 异源复合物 蛋白 42 PROTEIN (CAPSID PROTEIN GPF) × 6 (P03641) PROTEIN (SPIKE PROTEIN GPG) × 6 (P03643) PROTEIN (SCAFFOLDING PROTEIN GPB) × 6 (P03633) water × 42 与蛋白数一致
5 蛋白异源复合物 异源复合物 蛋白 7 PROTEIN (CAPSID PROTEIN GPF) × 1 (P03641) PROTEIN (SPIKE PROTEIN GPG) × 1 (P03643) PROTEIN (SCAFFOLDING PROTEIN GPB) × 1 (P03633) water × 7 与蛋白数一致
6 蛋白异源复合物 异源复合物 蛋白 280 PROTEIN (CAPSID PROTEIN GPF) × 40 (P03641) PROTEIN (SPIKE PROTEIN GPG) × 40 (P03643) PROTEIN (SCAFFOLDING PROTEIN GPB) × 40 (P03633) water × 280 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 VGD_BPPHX
Isoform —
PDB实体 1
链与序列区间 作者链 1; PDB构建体 1–152; UniProt 1–151 作者链 2; PDB构建体 1–152; UniProt 1–151 作者链 3; PDB构建体 1–152; UniProt 1–151 作者链 4; PDB构建体 1–152; UniProt 1–151

PROTEIN (CAPSID PROTEIN GPF)

物种未注明

UniProt P03641

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 420 PROTEIN (SCAFFOLDING PROTEIN GPD) × 240 (P69486) PROTEIN (SPIKE PROTEIN GPG) × 60 (P03643) PROTEIN (SCAFFOLDING PROTEIN GPB) × 60 (P03633) water × 420 与蛋白数一致
2 蛋白异源复合物 异源复合物 蛋白 7 PROTEIN (SCAFFOLDING PROTEIN GPD) × 4 (P69486) PROTEIN (SPIKE PROTEIN GPG) × 1 (P03643) PROTEIN (SCAFFOLDING PROTEIN GPB) × 1 (P03633) water × 7 与蛋白数一致
3 蛋白异源复合物 异源复合物 蛋白 35 PROTEIN (SCAFFOLDING PROTEIN GPD) × 20 (P69486) PROTEIN (SPIKE PROTEIN GPG) × 5 (P03643) PROTEIN (SCAFFOLDING PROTEIN GPB) × 5 (P03633) water × 35 与蛋白数一致
4 蛋白异源复合物 异源复合物 蛋白 42 PROTEIN (SCAFFOLDING PROTEIN GPD) × 24 (P69486) PROTEIN (SPIKE PROTEIN GPG) × 6 (P03643) PROTEIN (SCAFFOLDING PROTEIN GPB) × 6 (P03633) water × 42 与蛋白数一致
5 蛋白异源复合物 异源复合物 蛋白 7 PROTEIN (SCAFFOLDING PROTEIN GPD) × 4 (P69486) PROTEIN (SPIKE PROTEIN GPG) × 1 (P03643) PROTEIN (SCAFFOLDING PROTEIN GPB) × 1 (P03633) water × 7 与蛋白数一致
6 蛋白异源复合物 异源复合物 蛋白 280 PROTEIN (SCAFFOLDING PROTEIN GPD) × 160 (P69486) PROTEIN (SPIKE PROTEIN GPG) × 40 (P03643) PROTEIN (SCAFFOLDING PROTEIN GPB) × 40 (P03633) water × 280 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 VGF_BPPHX
Isoform —
PDB实体 2
链与序列区间 作者链 F; PDB构建体 1–426; UniProt 1–426

PROTEIN (SPIKE PROTEIN GPG)

物种未注明

UniProt P03643

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 420 PROTEIN (SCAFFOLDING PROTEIN GPD) × 240 (P69486) PROTEIN (CAPSID PROTEIN GPF) × 60 (P03641) PROTEIN (SCAFFOLDING PROTEIN GPB) × 60 (P03633) water × 420 与蛋白数一致
2 蛋白异源复合物 异源复合物 蛋白 7 PROTEIN (SCAFFOLDING PROTEIN GPD) × 4 (P69486) PROTEIN (CAPSID PROTEIN GPF) × 1 (P03641) PROTEIN (SCAFFOLDING PROTEIN GPB) × 1 (P03633) water × 7 与蛋白数一致
3 蛋白异源复合物 异源复合物 蛋白 35 PROTEIN (SCAFFOLDING PROTEIN GPD) × 20 (P69486) PROTEIN (CAPSID PROTEIN GPF) × 5 (P03641) PROTEIN (SCAFFOLDING PROTEIN GPB) × 5 (P03633) water × 35 与蛋白数一致
4 蛋白异源复合物 异源复合物 蛋白 42 PROTEIN (SCAFFOLDING PROTEIN GPD) × 24 (P69486) PROTEIN (CAPSID PROTEIN GPF) × 6 (P03641) PROTEIN (SCAFFOLDING PROTEIN GPB) × 6 (P03633) water × 42 与蛋白数一致
5 蛋白异源复合物 异源复合物 蛋白 7 PROTEIN (SCAFFOLDING PROTEIN GPD) × 4 (P69486) PROTEIN (CAPSID PROTEIN GPF) × 1 (P03641) PROTEIN (SCAFFOLDING PROTEIN GPB) × 1 (P03633) water × 7 与蛋白数一致
6 蛋白异源复合物 异源复合物 蛋白 280 PROTEIN (SCAFFOLDING PROTEIN GPD) × 160 (P69486) PROTEIN (CAPSID PROTEIN GPF) × 40 (P03641) PROTEIN (SCAFFOLDING PROTEIN GPB) × 40 (P03633) water × 280 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 VGG_BPPHX
Isoform —
PDB实体 3
链与序列区间 作者链 G; PDB构建体 1–175; UniProt 1–175

PROTEIN (SCAFFOLDING PROTEIN GPB)

物种未注明

UniProt P03633

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 420 PROTEIN (SCAFFOLDING PROTEIN GPD) × 240 (P69486) PROTEIN (CAPSID PROTEIN GPF) × 60 (P03641) PROTEIN (SPIKE PROTEIN GPG) × 60 (P03643) water × 420 与蛋白数一致
2 蛋白异源复合物 异源复合物 蛋白 7 PROTEIN (SCAFFOLDING PROTEIN GPD) × 4 (P69486) PROTEIN (CAPSID PROTEIN GPF) × 1 (P03641) PROTEIN (SPIKE PROTEIN GPG) × 1 (P03643) water × 7 与蛋白数一致
3 蛋白异源复合物 异源复合物 蛋白 35 PROTEIN (SCAFFOLDING PROTEIN GPD) × 20 (P69486) PROTEIN (CAPSID PROTEIN GPF) × 5 (P03641) PROTEIN (SPIKE PROTEIN GPG) × 5 (P03643) water × 35 与蛋白数一致
4 蛋白异源复合物 异源复合物 蛋白 42 PROTEIN (SCAFFOLDING PROTEIN GPD) × 24 (P69486) PROTEIN (CAPSID PROTEIN GPF) × 6 (P03641) PROTEIN (SPIKE PROTEIN GPG) × 6 (P03643) water × 42 与蛋白数一致
5 蛋白异源复合物 异源复合物 蛋白 7 PROTEIN (SCAFFOLDING PROTEIN GPD) × 4 (P69486) PROTEIN (CAPSID PROTEIN GPF) × 1 (P03641) PROTEIN (SPIKE PROTEIN GPG) × 1 (P03643) water × 7 与蛋白数一致
6 蛋白异源复合物 异源复合物 蛋白 280 PROTEIN (SCAFFOLDING PROTEIN GPD) × 160 (P69486) PROTEIN (CAPSID PROTEIN GPF) × 40 (P03641) PROTEIN (SPIKE PROTEIN GPG) × 40 (P03643) water × 280 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 VGB_BPPHX
Isoform —
PDB实体 4
链与序列区间 作者链 B; PDB构建体 1–120; UniProt 1–120

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。

▼

2. 结构基本信息 2. Structure Basics

条目编号 entry_id1cd3
沉积日期 deposition_date1999-03-05
结构标题 titlePROCAPSID OF BACTERIOPHAGE PHIX174
关键词 keywordsCOMPLEX (VIRUS CAPSID PROTEINS), BACTERIOPHAGE, PROCAPSID, SCAFFOLDING PROTEIN, CHAPERONE, Icosahedral virus, Virus; VIRUS
实验方法 methodX-RAY DIFFRACTION
▼

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。

1cd3__assembly_1__model_1

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

下载该曲线 .dat

1cd3__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 109 1010 1011 q (1/Angstrom) I(q)
100 个绘图点;横轴和纵轴均采用对数尺度。

1cd3__assembly_1__model_1 | P(r) · Pending

新版 assembly/model P(r) 尚未计算 此处仅保留位置,不展示旧数据 r (Angstrom) P(r)
P(r) 将按相同 assembly/model 分别计算和展示。
Rg(Guinier)0.00 Å
Rg(电子密度)138.90 Å
总 Rg139.00 Å
原子数585300
残基数73980
排除体积10394000 ų
最大 q0.500 Å⁻¹
Assembly Model 结构单元 聚集说明 状态 CRYSOL 操作
1 1 1cd3__assembly_1__model_1 420-MERIC (420) 成功 4.1.3-1-20251215 (887e7ef) 查看 下载
2 1 1cd3__assembly_2__model_1 heptameric (7) 排除 — —
排除原因: 辅助对称表示,不是完整或代表性的 biological assembly。
3 1 1cd3__assembly_3__model_1 35-meric (35) 排除 — —
排除原因: 辅助对称表示,不是完整或代表性的 biological assembly。
4 1 1cd3__assembly_4__model_1 42-meric (42) 排除 — —
排除原因: 辅助对称表示,不是完整或代表性的 biological assembly。
5 1 1cd3__assembly_5__model_1 heptameric (7) 排除 — —
排除原因: 辅助对称表示,不是完整或代表性的 biological assembly。
6 1 1cd3__assembly_6__model_1 280-meric (280) 排除 — —
排除原因: 辅助对称表示,不是完整或代表性的 biological assembly。
▶

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

▶

5. 实体与聚合物信息 Entities & Polymers (5)

▼

6. 折叠分类 (SCOP + CATH) 13 domains

SCOP 2.08 (6 domains)

结构域编号 domain_idd1cd31_
类 Class classa — All alpha proteins
折叠类型 Fold folda.84 — Scaffolding protein gpD of bacteriophage procapsid
超家族 Superfamily superfamilya.84.1 — Scaffolding protein gpD of bacteriophage procapsid
家族 Family familya.84.1.1 — Scaffolding protein gpD of bacteriophage procapsid
结构域编号 domain_idd1cd32_
类 Class classa — All alpha proteins
折叠类型 Fold folda.84 — Scaffolding protein gpD of bacteriophage procapsid
超家族 Superfamily superfamilya.84.1 — Scaffolding protein gpD of bacteriophage procapsid
家族 Family familya.84.1.1 — Scaffolding protein gpD of bacteriophage procapsid
结构域编号 domain_idd1cd33_
类 Class classa — All alpha proteins
折叠类型 Fold folda.84 — Scaffolding protein gpD of bacteriophage procapsid
超家族 Superfamily superfamilya.84.1 — Scaffolding protein gpD of bacteriophage procapsid
家族 Family familya.84.1.1 — Scaffolding protein gpD of bacteriophage procapsid
结构域编号 domain_idd1cd34_
类 Class classa — All alpha proteins
折叠类型 Fold folda.84 — Scaffolding protein gpD of bacteriophage procapsid
超家族 Superfamily superfamilya.84.1 — Scaffolding protein gpD of bacteriophage procapsid
家族 Family familya.84.1.1 — Scaffolding protein gpD of bacteriophage procapsid
结构域编号 domain_idd1cd3f_
类 Class classb — All beta proteins
折叠类型 Fold foldb.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
超家族 Superfamily superfamilyb.121.5 — ssDNA viruses
家族 Family familyb.121.5.1 — Microviridae-like VP
结构域编号 domain_idd1cd3g_
类 Class classb — All beta proteins
折叠类型 Fold foldb.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
超家族 Superfamily superfamilyb.121.5 — ssDNA viruses
家族 Family familyb.121.5.1 — Microviridae-like VP

CATH v4.4 (7 domains)

结构域编号 domain_id1cd3100
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology1850 — Procapsid Of Bacteriophage Phix174, Chain 1
同源超家族 H-superfamily homologous superfamily10 — Scaffold protein D
结构域编号 domain_id1cd3200
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology1850 — Procapsid Of Bacteriophage Phix174, Chain 1
同源超家族 H-superfamily homologous superfamily10 — Scaffold protein D
结构域编号 domain_id1cd3300
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology1850 — Procapsid Of Bacteriophage Phix174, Chain 1
同源超家族 H-superfamily homologous superfamily10 — Scaffold protein D
结构域编号 domain_id1cd3400
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology1850 — Procapsid Of Bacteriophage Phix174, Chain 1
同源超家族 H-superfamily homologous superfamily10 — Scaffold protein D
结构域编号 domain_id1cd3B00
类 Class class4 — Few Secondary Structures
架构 Architecture architecture10 — Irregular
拓扑 Topology topology1260 — Scaffolding protein gpD of bacteriophage procapsid fold
同源超家族 H-superfamily homologous superfamily10 — Scaffolding protein gpD of bacteriophage procapsid
结构域编号 domain_id1cd3F00
类 Class class2 — Mainly Beta
架构 Architecture architecture60 — Sandwich
拓扑 Topology topology169 — Bacteriophage G4 Capsid Proteins Gpf, Gpg, Gpj, subunit 1
同源超家族 H-superfamily homologous superfamily10 — Microviridae F protein
结构域编号 domain_id1cd3G00
类 Class class2 — Mainly Beta
架构 Architecture architecture60 — Sandwich
拓扑 Topology topology120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily20 —
▶

7. 引用文献 (7)