3iqf

Structure of F420 dependent methylene-tetrahydromethanopterin dehydrogenase in complex with methenyl-tetrahydromethanopterin

Method: X-RAY DIFFRACTION

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

F420-dependent methylenetetrahydromethanopterin dehydrogenase

Methanopyrus kandleri

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 6	;1-{4-[(6S,6aR,7R)-3-amino-6,7-dimethyl-1-oxo-1,2,5,6,6a,7-hexahydro-8H-imidazo[1,5-f]pteridin-10-ium-8-yl]phenyl}-1-deoxy-5-O-{5-O-[(S)-{[(1S)-1,3-dicarboxypropyl]oxy}(hydroxy)phosphoryl]-alpha-D-ribofuranosyl}-D-ribitol ; × 6 CALCIUM ION × 2 SODIUM ION × 1 water × 6	与蛋白数一致
2	蛋白同源多聚体	同源多聚体	蛋白 6	;1-{4-[(6S,6aR,7R)-3-amino-6,7-dimethyl-1-oxo-1,2,5,6,6a,7-hexahydro-8H-imidazo[1,5-f]pteridin-10-ium-8-yl]phenyl}-1-deoxy-5-O-{5-O-[(S)-{[(1S)-1,3-dicarboxypropyl]oxy}(hydroxy)phosphoryl]-alpha-D-ribofuranosyl}-D-ribitol ; × 6 CALCIUM ION × 5 water × 6	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	MTD_METKA
Isoform	—
PDB实体	1
链与序列区间	作者链 A； PDB构建体 1–283； UniProt 1–283 作者链 B； PDB构建体 1–283； UniProt 1–283 作者链 C； PDB构建体 1–283； UniProt 1–283 作者链 D； PDB构建体 1–283； UniProt 1–283 作者链 E； PDB构建体 1–283； UniProt 1–283 作者链 F； PDB构建体 1–283； UniProt 1–283 作者链 G； PDB构建体 1–283； UniProt 1–283 作者链 H； PDB构建体 1–283； UniProt 1–283 作者链 I； PDB构建体 1–283； UniProt 1–283 作者链 J； PDB构建体 1–283； UniProt 1–283 作者链 K； PDB构建体 1–283； UniProt 1–283 作者链 L； PDB构建体 1–283； UniProt 1–283

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	3iqf
沉积日期 deposition_date	2009-08-20
结构标题 title	Structure of F420 dependent methylene-tetrahydromethanopterin dehydrogenase in complex with methenyl-tetrahydromethanopterin
关键词 keywords	binary complex of protein and substrate, Methanogenesis, One-carbon metabolism, Oxidoreductase; OXIDOREDUCTASE
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。

3iqf__assembly_1__model_1

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

下载该曲线 .dat

3iqf__assembly_1__model_1 | I(q)

100 个绘图点；横轴和纵轴均采用对数尺度。

3iqf__assembly_1__model_1 | P(r) · Pending

P(r) 将按相同 assembly/model 分别计算和展示。

Rg（Guinier）	35.89 Å
Rg（电子密度）	35.01 Å
总 Rg	35.40 Å
原子数	13365
残基数	1692
排除体积	238130 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	`3iqf__assembly_1__model_1`	hexameric （6）	成功	4.1.3-1-20251215 (887e7ef)	查看下载
2	1	`3iqf__assembly_2__model_1`	hexameric （6）	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	F420-dependent methylenetetrahydromethanopterin dehydrogenase
分子量 formula_weight	31415.9 kDa
EC 编号 ec_number	1.5.99.9
来源方法 src_method	man
拷贝数 entity_count	12

聚合物 Polymer

聚合物类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F,G,H,I,J,K,L
原子数 atom_count	27835

MTVAKAIFIKCGNLGTSMMMDMLLDERADREDVEFRVVGTSVKMDPECVEAAVEMALDIAEDFEPDFIVYGGPNPAAPGPSKAREMLADSEYPAVIIGDAPGLKVKDEMEEQGLGYILVKPDAMLGARREFLDPVEMAIYNADLMKVLAATGVFRVVQEAFDELIEKAKEDEISENDLPKLVIDRNTLLEREEFENPYAMVKAMAALEIAENVADVSVEGCFVEQDKERYVPIVASAHEMMRKAAELADEARELEKSNDAVLRTPHAPDGKVLSKRKFMEDPE

来源 Source

来源生物 organism	Methanopyrus kandleri
NCBI 分类编号 ncbi_taxonomy_id	2320
宿主生物 host_organism	Escherichia coli

实体 2 Entity 2 non-polymer

描述 description	;1-{4-[(6S,6aR,7R)-3-amino-6,7-dimethyl-1-oxo-1,2,5,6,6a,7-hexahydro-8H-imidazo[1,5-f]pteridin-10-ium-8-yl]phenyl}-1-deoxy-5-O-{5-O-[(S)-{[(1S)-1,3-dicarboxypropyl]oxy}(hydroxy)phosphoryl]-alpha-D-ribofuranosyl}-D-ribitol ;
分子量 formula_weight	787.7 kDa
来源方法 src_method	syn
拷贝数 entity_count	12

实体 3 Entity 3 non-polymer

描述 description	CALCIUM ION
分子量 formula_weight	40.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	7

实体 4 Entity 4 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 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	1068

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6. 折叠分类 (SCOP + CATH) 36 domains

SCOP 2.08 (12 domains)

结构域编号 domain_id	d3iqfa_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.127 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
超家族 Superfamily superfamily	c.127.1 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
家族 Family family	c.127.1.1 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)

结构域编号 domain_id	d3iqfb_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.127 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
超家族 Superfamily superfamily	c.127.1 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
家族 Family family	c.127.1.1 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)

结构域编号 domain_id	d3iqfc_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.127 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
超家族 Superfamily superfamily	c.127.1 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
家族 Family family	c.127.1.1 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)

结构域编号 domain_id	d3iqfd_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.127 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
超家族 Superfamily superfamily	c.127.1 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
家族 Family family	c.127.1.1 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)

结构域编号 domain_id	d3iqfe_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.127 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
超家族 Superfamily superfamily	c.127.1 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
家族 Family family	c.127.1.1 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)

结构域编号 domain_id	d3iqff_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.127 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
超家族 Superfamily superfamily	c.127.1 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
家族 Family family	c.127.1.1 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)

结构域编号 domain_id	d3iqfg_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.127 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
超家族 Superfamily superfamily	c.127.1 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
家族 Family family	c.127.1.1 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)

结构域编号 domain_id	d3iqfh_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.127 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
超家族 Superfamily superfamily	c.127.1 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
家族 Family family	c.127.1.1 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)

结构域编号 domain_id	d3iqfi_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.127 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
超家族 Superfamily superfamily	c.127.1 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
家族 Family family	c.127.1.1 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)

结构域编号 domain_id	d3iqfj_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.127 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
超家族 Superfamily superfamily	c.127.1 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
家族 Family family	c.127.1.1 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)

结构域编号 domain_id	d3iqfk_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.127 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
超家族 Superfamily superfamily	c.127.1 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
家族 Family family	c.127.1.1 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)

结构域编号 domain_id	d3iqfl_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.127 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
超家族 Superfamily superfamily	c.127.1 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
家族 Family family	c.127.1.1 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)

CATH v4.4 (24 domains)

结构域编号 domain_id	3iqfA01
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	10830 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)

结构域编号 domain_id	3iqfA02
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	120 —

结构域编号 domain_id	3iqfB01
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	10830 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)

结构域编号 domain_id	3iqfB02
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	120 —

结构域编号 domain_id	3iqfC01
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	10830 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)

结构域编号 domain_id	3iqfC02
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	120 —

结构域编号 domain_id	3iqfD01
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	10830 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)

结构域编号 domain_id	3iqfD02
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	120 —

结构域编号 domain_id	3iqfE01
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	10830 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)

结构域编号 domain_id	3iqfE02
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	120 —

结构域编号 domain_id	3iqfF01
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	10830 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)

结构域编号 domain_id	3iqfF02
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	120 —

结构域编号 domain_id	3iqfG01
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	10830 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)

结构域编号 domain_id	3iqfG02
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	120 —

结构域编号 domain_id	3iqfH01
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	10830 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)

结构域编号 domain_id	3iqfH02
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	120 —

结构域编号 domain_id	3iqfI01
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	10830 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)

结构域编号 domain_id	3iqfI02
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	120 —

结构域编号 domain_id	3iqfJ01
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	10830 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)

结构域编号 domain_id	3iqfJ02
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	120 —

结构域编号 domain_id	3iqfK01
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	10830 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)

结构域编号 domain_id	3iqfK02
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	120 —

结构域编号 domain_id	3iqfL01
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	10830 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)

结构域编号 domain_id	3iqfL02
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	120 —

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晶胞边长 a length_a	103.400 Å
晶胞边长 b length_b	167.100 Å
晶胞边长 c length_c	122.500 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	113.60 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	24

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	2.100 Å
最低分辨率 resolution_low	112.500 Å
R 因子 r_factor	0.1625
R_work r_work	0.1605
R_free r_free	0.2003

Structure of F420 dependent methylene-tetrahydromethanopterin dehydrogenase in complex with methenyl-tetrahydromethanopterin

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

F420-dependent methylenetetrahydromethanopterin dehydrogenase

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

3iqf__assembly_1__model_1

3iqf__assembly_1__model_1 | I(q)

3iqf__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 (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) 36 domains

SCOP 2.08 (12 domains)

CATH v4.4 (24 domains)

7. 引用文献 (1)

Structure of F420 dependent methylene-tetrahydromethanopterin dehydrogenase in complex with methenyl-tetrahydromethanopterin

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

F420-dependent methylenetetrahydromethanopterin dehydrogenase

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

3iqf__assembly_1__model_1

3iqf__assembly_1__model_1 | I(q)

3iqf__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 (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) 36 domains

SCOP 2.08 (12 domains)

CATH v4.4 (24 domains)

7. 引用文献 (1)