8brn

Crystal structure of red kidney bean purple acid phosphatase in complex with an alpha-aminonaphthylmethylphosphonic acid inhibitor

Method: X-RAY DIFFRACTION

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

Fe(3+)-Zn(2+) purple acid phosphatase

物种未注明

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	其他组合	同源多聚体	蛋白 2 其他聚合物 8	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ;alpha-D-mannopyranose-(1-2)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 ;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 3 ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ;beta-D-mannopyranose-(5-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 ZINC ION × 2 FE (III) ION × 2 CITRATE ANION × 8 TRIETHYLENE GLYCOL × 3 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 SULFATE ION × 14 1,2-ETHANEDIOL × 2 GLYCEROL × 25 CHLORIDE ION × 3 [(R)-(decanoylamino)-naphthalen-1-yl-methyl]phosphonic acid × 3 water × 2	与蛋白数一致
2	其他组合	同源多聚体	蛋白 2 其他聚合物 9	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 3 ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 ;alpha-D-mannopyranose-(1-2)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 alpha-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ZINC ION × 2 FE (III) ION × 2 CITRATE ANION × 5 TRIETHYLENE GLYCOL × 3 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 SULFATE ION × 18 1,2-ETHANEDIOL × 2 GLYCEROL × 25 CHLORIDE ION × 3 [(R)-(decanoylamino)-naphthalen-1-yl-methyl]phosphonic acid × 2 SODIUM ION × 1 DIMETHYL SULFOXIDE × 1 water × 2	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	PPAF_PHAVU
Isoform	—
PDB实体	1
链与序列区间	作者链 A； PDB构建体 1–428； UniProt 32–459 作者链 B； PDB构建体 1–428； UniProt 32–459 作者链 C； PDB构建体 1–428； UniProt 32–459 作者链 D； PDB构建体 1–428； UniProt 32–459

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	8brn
沉积日期 deposition_date	2022-11-23
结构标题 title	Crystal structure of red kidney bean purple acid phosphatase in complex with an alpha-aminonaphthylmethylphosphonic acid inhibitor
关键词 keywords	Metallohydrolase, Phosphatase, METAL BINDING PROTEIN; METAL BINDING 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。

8brn__assembly_1__model_1

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

下载该曲线 .dat

8brn__assembly_1__model_1 | I(q)

100 个绘图点；横轴和纵轴均采用对数尺度。

8brn__assembly_1__model_1 | P(r) · Pending

P(r) 将按相同 assembly/model 分别计算和展示。

Rg（Guinier）	31.52 Å
Rg（电子密度）	30.50 Å
总 Rg	31.38 Å
原子数	7894
残基数	853
排除体积	139080 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	`8brn__assembly_1__model_1`	dimeric （2）	成功	4.1.3-1-20251215 (887e7ef)	查看下载
2	1	`8brn__assembly_2__model_1`	dimeric （2）	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 (23)

实体 1 Entity 1 polymer

描述 description	Fe(3+)-Zn(2+) purple acid phosphatase
分子量 formula_weight	49770.6 kDa
EC 编号 ec_number	3.1.3.2
来源方法 src_method	nat
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	18800

TNKNRDMPLDSDVFRVPPGYNAPQQVHITQGDLVGRAMIISWVTMDEPGSSAVRYWSEKNGRKRIAKGKMSTYRFFNYSSGFIHHTTIRKLKYNTKYYYEVGLRNTTRRFSFITPPQTGLDVPYTFGLIGDLGQSFDSNTTLSHYELSPKKGQTVLFVGDLSYADRYPNHDNVRWDTWGRFTERSVAYQPWIWTAGNHEIEFAPEINETEPFKPFSYRYHVPYEASQSTSPFWYSIKRASAHIIVLSSYSAYGRGTPQYTWLKKELRKVKRSETPWLIVLMHSPLYNSYNHHFMEGEAMRTKFEAWFVKYKVDVVFAGHVHAYERSERVSNIAYKITNGLCTPVKDQSAPVYITIGDAGNYGVIDSNMIQPQPEYSAFREASFGHGMFDIKNRTHAHFSWNRNQDGVAVEADSVWFFNRHWYPVDDST

实体 2 Entity 2 branched

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	424.4 kDa
来源方法 src_method	man
拷贝数 entity_count	3

实体 3 Entity 3 branched

描述 description	;alpha-D-mannopyranose-(1-2)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	1057.0 kDa
来源方法 src_method	man
拷贝数 entity_count	1

实体 4 Entity 4 branched

描述 description	;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	732.7 kDa
来源方法 src_method	man
拷贝数 entity_count	6

实体 5 Entity 5 branched

描述 description	;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	1057.0 kDa
来源方法 src_method	man
拷贝数 entity_count	2

实体 6 Entity 6 branched

描述 description	;alpha-D-mannopyranose-(1-2)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	894.8 kDa
来源方法 src_method	man
拷贝数 entity_count	1

实体 7 Entity 7 branched

描述 description	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	586.5 kDa
来源方法 src_method	man
拷贝数 entity_count	1

实体 8 Entity 8 branched

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	424.4 kDa
来源方法 src_method	man
拷贝数 entity_count	1

实体 9 Entity 9 branched

描述 description	;beta-D-mannopyranose-(5-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	732.7 kDa
来源方法 src_method	man
拷贝数 entity_count	1

实体 10 Entity 10 branched

描述 description	alpha-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	367.3 kDa
来源方法 src_method	man
拷贝数 entity_count	1

实体 11 Entity 11 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	man
拷贝数 entity_count	4

实体 12 Entity 12 non-polymer

描述 description	FE (III) ION
分子量 formula_weight	55.8 kDa
来源方法 src_method	man
拷贝数 entity_count	4

实体 13 Entity 13 non-polymer

描述 description	CITRATE ANION
分子量 formula_weight	189.1 kDa
来源方法 src_method	man
拷贝数 entity_count	13

实体 14 Entity 14 non-polymer

描述 description	TRIETHYLENE GLYCOL
分子量 formula_weight	150.2 kDa
来源方法 src_method	man
拷贝数 entity_count	6

实体 15 Entity 15 non-polymer

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	221.2 kDa
来源方法 src_method	man
拷贝数 entity_count	5

实体 16 Entity 16 non-polymer

描述 description	SULFATE ION
分子量 formula_weight	96.1 kDa
来源方法 src_method	man
拷贝数 entity_count	32

实体 17 Entity 17 non-polymer

描述 description	1,2-ETHANEDIOL
分子量 formula_weight	62.1 kDa
来源方法 src_method	man
拷贝数 entity_count	4

实体 18 Entity 18 non-polymer

描述 description	GLYCEROL
分子量 formula_weight	92.1 kDa
来源方法 src_method	man
拷贝数 entity_count	50

实体 19 Entity 19 non-polymer

描述 description	CHLORIDE ION
分子量 formula_weight	35.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

实体 20 Entity 20 non-polymer

描述 description	[(R)-(decanoylamino)-naphthalen-1-yl-methyl]phosphonic acid
分子量 formula_weight	391.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	5

实体 21 Entity 21 non-polymer

描述 description	SODIUM ION
分子量 formula_weight	23.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

实体 22 Entity 22 non-polymer

描述 description	DIMETHYL SULFOXIDE
分子量 formula_weight	78.1 kDa
来源方法 src_method	man
拷贝数 entity_count	1

实体 23 Entity 23 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	2663

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晶胞边长 a length_a	125.859 Å
晶胞边长 b length_b	125.859 Å
晶胞边长 c length_c	298.339 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	24

空间群 space_group	P 31 2 1
空间群编号 int_tables_number	152
晶系 crystal_system	trigonal

分辨率 resolution	2.000 Å
最低分辨率 resolution_low	19.960 Å
R 因子 r_factor	0.1593
R_work r_work	0.1568
R_free r_free	0.2062