1u6j

The Structure of native coenzyme F420-dependent methylenetetrahydromethanopterin dehydrogenase at 2.4A resolution

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

F420-dependent methylenetetrahydromethanopterin dehydrogenase

Methanopyrus kandleri

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	MAGNESIUM ION × 4 water × 6	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 6	MAGNESIUM ION × 4 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MTD_METKA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–283； UniProt 1–282 Author chain B； PDBConstruct 2–283； UniProt 1–282 Author chain C； PDBConstruct 2–283； UniProt 1–282 Author chain D； PDBConstruct 2–283； UniProt 1–282 Author chain E； PDBConstruct 2–283； UniProt 1–282 Author chain F； PDBConstruct 2–283； UniProt 1–282 Author chain G； PDBConstruct 2–283； UniProt 1–282 Author chain H； PDBConstruct 2–283； UniProt 1–282 Author chain I； PDBConstruct 2–283； UniProt 1–282 Author chain J； PDBConstruct 2–283； UniProt 1–282 Author chain K； PDBConstruct 2–283； UniProt 1–282 Author chain L； PDBConstruct 2–283； UniProt 1–282

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1u6j
Deposition date deposition_date	2004-07-30
Structure title title	The Structure of native coenzyme F420-dependent methylenetetrahydromethanopterin dehydrogenase at 2.4A resolution
Keywords keywords	MONOMER: ALPHA/BETA DOMAIN, HELIX BUNDLE; TRIMER OF DIMERS, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

1u6j__assembly_1__model_1

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

Download this curve (.dat)

1u6j__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1u6j__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	35.87 Å
Rg (electron density)	35.00 Å
Total Rg	35.35 Å
Atom count	13096
Residues	1692
Excluded volume	233570 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1u6j__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1u6j__assembly_2__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	F420-dependent methylenetetrahydromethanopterin dehydrogenase
Molecular weight formula_weight	31415.9 kDa
EC 编号 ec_number	1.5.99.9
Source method src_method	man
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L
Atom count atom_count	26753

MTVAKAIFIKCGNLGTSMMMDMLLDERADREDVEFRVVGTSVKMDPECVEAAVEMALDIAEDFEPDFIVYGGPNPAAPGPSKAREMLADSEYPAVIIGDAPGLKVKDEMEEQGLGYILVKPDAMLGARREFLDPVEMAIYNADLMKVLAATGVFRVVQEAFDELIEKAKEDEISENDLPKLVIDRNTLLEREEFENPYAMVKAMAALEIAENVADVSVEGCFVEQDKERYVPIVASAHEMMRKAAELADEARELEKSNDAVLRTPHAPDGKVLSKRKFMEDPE

Source Source

Source organism organism	Methanopyrus kandleri
NCBI taxonomy ID ncbi_taxonomy_id	2320
Host organism host_organism	Escherichia coli BL21

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	561

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6. Fold Classification (SCOP + CATH) 36 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d1u6ja_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.127 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
Superfamily Superfamily superfamily	c.127.1 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
Family Family family	c.127.1.1 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)

Domain ID domain_id	d1u6jb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.127 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
Superfamily Superfamily superfamily	c.127.1 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
Family Family family	c.127.1.1 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)

Domain ID domain_id	d1u6jc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.127 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
Superfamily Superfamily superfamily	c.127.1 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
Family Family family	c.127.1.1 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)

Domain ID domain_id	d1u6jd_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.127 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
Superfamily Superfamily superfamily	c.127.1 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
Family Family family	c.127.1.1 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)

Domain ID domain_id	d1u6je_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.127 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
Superfamily Superfamily superfamily	c.127.1 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
Family Family family	c.127.1.1 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)

Domain ID domain_id	d1u6jf_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.127 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
Superfamily Superfamily superfamily	c.127.1 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
Family Family family	c.127.1.1 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)

Domain ID domain_id	d1u6jg_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.127 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
Superfamily Superfamily superfamily	c.127.1 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
Family Family family	c.127.1.1 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)

Domain ID domain_id	d1u6jh_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.127 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
Superfamily Superfamily superfamily	c.127.1 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
Family Family family	c.127.1.1 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)

Domain ID domain_id	d1u6ji_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.127 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
Superfamily Superfamily superfamily	c.127.1 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
Family Family family	c.127.1.1 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)

Domain ID domain_id	d1u6jj_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.127 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
Superfamily Superfamily superfamily	c.127.1 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
Family Family family	c.127.1.1 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)

Domain ID domain_id	d1u6jk_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.127 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
Superfamily Superfamily superfamily	c.127.1 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
Family Family family	c.127.1.1 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)

Domain ID domain_id	d1u6jl_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.127 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
Superfamily Superfamily superfamily	c.127.1 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
Family Family family	c.127.1.1 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)

CATH v4.4 (24 domains)

Domain ID domain_id	1u6jA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10830 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)

Domain ID domain_id	1u6jA02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	120 —

Domain ID domain_id	1u6jB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10830 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)

Domain ID domain_id	1u6jB02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	120 —

Domain ID domain_id	1u6jC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10830 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)

Domain ID domain_id	1u6jC02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	120 —

Domain ID domain_id	1u6jD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10830 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)

Domain ID domain_id	1u6jD02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	120 —

Domain ID domain_id	1u6jE01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10830 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)

Domain ID domain_id	1u6jE02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	120 —

Domain ID domain_id	1u6jF01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10830 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)

Domain ID domain_id	1u6jF02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	120 —

Domain ID domain_id	1u6jG01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10830 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)

Domain ID domain_id	1u6jG02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	120 —

Domain ID domain_id	1u6jH01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10830 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)

Domain ID domain_id	1u6jH02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	120 —

Domain ID domain_id	1u6jI01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10830 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)

Domain ID domain_id	1u6jI02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	120 —

Domain ID domain_id	1u6jJ01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10830 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)

Domain ID domain_id	1u6jJ02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	120 —

Domain ID domain_id	1u6jK01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10830 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)

Domain ID domain_id	1u6jK02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	120 —

Domain ID domain_id	1u6jL01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10830 — F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)

Domain ID domain_id	1u6jL02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	120 —

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Unit-cell length a length_a	150.900 Å
Unit-cell length b length_b	118.900 Å
Unit-cell length c length_c	219.200 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.01 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	48

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.1750
R_free r_free	0.2350

The Structure of native coenzyme F420-dependent methylenetetrahydromethanopterin dehydrogenase at 2.4A resolution

1. Protein Identity and Related Structures Protein Identity & Related Structures

F420-dependent methylenetetrahydromethanopterin dehydrogenase

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1u6j__assembly_1__model_1

1u6j__assembly_1__model_1 | I(q)

1u6j__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 36 domains

SCOP 2.08 (12 domains)

CATH v4.4 (24 domains)

7. Citations (2)

The Structure of native coenzyme F420-dependent methylenetetrahydromethanopterin dehydrogenase at 2.4A resolution

1. Protein Identity and Related Structures Protein Identity & Related Structures

F420-dependent methylenetetrahydromethanopterin dehydrogenase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1u6j__assembly_1__model_1

1u6j__assembly_1__model_1 | I(q)

1u6j__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 36 domains

SCOP 2.08 (12 domains)

CATH v4.4 (24 domains)

7. Citations (2)