2fhj

Crystal structure of formylmethanofuran: tetrahydromethanopterin formyltransferase in complex with its coenzymes

Method: X-RAY DIFFRACTION

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

Formylmethanofuran--tetrahydromethanopterin formyltransferase

Methanopyrus kandleri

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	POTASSIUM ION × 17 N-[4,5,7-TRICARBOXYHEPTANOYL]-L-GAMMA-GLUTAMYL-N-{2-[4-({5-[(FORMYLAMINO)METHYL]-3-FURYL}METHOXY)PHENYL]ETHYL}-D-GLUTAMINE × 4 ;5-(4-{[1-(2-AMINO-5-FORMYL-7-METHYL-4-OXO-3,4,5,6,7,8-HEXAHYDROPTERIDIN-6-YL)ETHYL]AMINO}PHENYL)-5-DEOXY-1-O-{5-O-[(1,3-DICARBOXYPROPOXY)(HYDROXY)PHOSPHORYL]PENTOFURANOSYL}PENTITOL ; × 2 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL × 3 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	FTR_METKA
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–296； UniProt 1–296 Author chain B； PDBConstruct 1–296； UniProt 1–296 Author chain C； PDBConstruct 1–296； UniProt 1–296 Author chain D； PDBConstruct 1–296； UniProt 1–296

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	2fhj
Deposition date deposition_date	2005-12-25
Structure title title	Crystal structure of formylmethanofuran: tetrahydromethanopterin formyltransferase in complex with its coenzymes
Keywords keywords	tetrahydromethanopterin; methanofuran; C1 metabolism; formyltransferase; complex, TRANSFERASE; TRANSFERASE
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.

2fhj__assembly_1__model_1

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

Download this curve (.dat)

2fhj__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2fhj__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.47 Å
Rg (electron density)	29.06 Å
Total Rg	29.68 Å
Atom count	9045
Residues	1183
Excluded volume	161550 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2fhj__assembly_1__model_1`	tetrameric （4）	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 (8)

Entity 1 Entity 1 polymer

Description description	Formylmethanofuran--tetrahydromethanopterin formyltransferase
Molecular weight formula_weight	31686.4 kDa
EC 编号 ec_number	2.3.1.101
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	9818

MEINGVEIEDTFAEAFEAKMARVLITAASHKWAMIAVKEATGFGTSVIMCPAEAGIDCGYVPPEETPDGRPGVTIMIGHNDEDELKEQLLDRIGQCVMTAPTASAFDAMPEAEKEDEDRVGYKLSFFGDGYQEEDELDGRKVWKIPVVEGEFIVEDSFGITTGVAGGNFYIMAESQPAGLQAAEAAVDAIKGVEGAYAPFPGGIVASASKVGSKQYDFLPASTNDAYCPTVEDNELPEGVKCVYEIVINGLNEEAVKEAMRVGIEAACQQPGVVKISAGNFGGKLGQYEIHLHDLF

Source Source

Source organism organism	Methanopyrus kandleri
NCBI taxonomy ID ncbi_taxonomy_id	2320
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Formylmethanofuran--tetrahydromethanopterin formyltransferase
Molecular weight formula_weight	31702.4 kDa
EC 编号 ec_number	2.3.1.101
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

Source Source

Source organism organism	Methanopyrus kandleri
NCBI taxonomy ID ncbi_taxonomy_id	2320
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	17

Entity 4 Entity 4 non-polymer

Description description	N-[4,5,7-TRICARBOXYHEPTANOYL]-L-GAMMA-GLUTAMYL-N-{2-[4-({5-[(FORMYLAMINO)METHYL]-3-FURYL}METHOXY)PHENYL]ETHYL}-D-GLUTAMINE
Molecular weight formula_weight	776.7 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	;5-(4-{[1-(2-AMINO-5-FORMYL-7-METHYL-4-OXO-3,4,5,6,7,8-HEXAHYDROPTERIDIN-6-YL)ETHYL]AMINO}PHENYL)-5-DEOXY-1-O-{5-O-[(1,3-DICARBOXYPROPOXY)(HYDROXY)PHOSPHORYL]PENTOFURANOSYL}PENTITOL ;
Molecular weight formula_weight	804.7 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
Molecular weight formula_weight	354.4 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 7 Entity 7 non-polymer

Description description	3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL
Molecular weight formula_weight	634.8 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	451

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d2fhja1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.33 — Formylmethanofuran:tetrahydromethanopterin formyltransferase
Family Family family	d.58.33.1 — Formylmethanofuran:tetrahydromethanopterin formyltransferase

Domain ID domain_id	d2fhja2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.33 — Formylmethanofuran:tetrahydromethanopterin formyltransferase
Family Family family	d.58.33.1 — Formylmethanofuran:tetrahydromethanopterin formyltransferase

Domain ID domain_id	d2fhjb1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.33 — Formylmethanofuran:tetrahydromethanopterin formyltransferase
Family Family family	d.58.33.1 — Formylmethanofuran:tetrahydromethanopterin formyltransferase

Domain ID domain_id	d2fhjb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.33 — Formylmethanofuran:tetrahydromethanopterin formyltransferase
Family Family family	d.58.33.1 — Formylmethanofuran:tetrahydromethanopterin formyltransferase

Domain ID domain_id	d2fhjc1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.33 — Formylmethanofuran:tetrahydromethanopterin formyltransferase
Family Family family	d.58.33.1 — Formylmethanofuran:tetrahydromethanopterin formyltransferase

Domain ID domain_id	d2fhjc2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.33 — Formylmethanofuran:tetrahydromethanopterin formyltransferase
Family Family family	d.58.33.1 — Formylmethanofuran:tetrahydromethanopterin formyltransferase

Domain ID domain_id	d2fhjd1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.33 — Formylmethanofuran:tetrahydromethanopterin formyltransferase
Family Family family	d.58.33.1 — Formylmethanofuran:tetrahydromethanopterin formyltransferase

Domain ID domain_id	d2fhjd2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.33 — Formylmethanofuran:tetrahydromethanopterin formyltransferase
Family Family family	d.58.33.1 — Formylmethanofuran:tetrahydromethanopterin formyltransferase

CATH v4.4 (8 domains)

Domain ID domain_id	2fhjA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	520 —

Domain ID domain_id	2fhjA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	520 —

Domain ID domain_id	2fhjB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	520 —

Domain ID domain_id	2fhjB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	520 —

Domain ID domain_id	2fhjC01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	520 —

Domain ID domain_id	2fhjC02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	520 —

Domain ID domain_id	2fhjD01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	520 —

Domain ID domain_id	2fhjD02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	520 —

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Unit-cell length a length_a	85.000 Å
Unit-cell length b length_b	74.150 Å
Unit-cell length c length_c	103.870 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	113.54 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2210
R_work r_work	0.2190
R_free r_free	0.2560

Crystal structure of formylmethanofuran: tetrahydromethanopterin formyltransferase in complex with its coenzymes

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

Formylmethanofuran--tetrahydromethanopterin formyltransferase

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

2fhj__assembly_1__model_1

2fhj__assembly_1__model_1 | I(q)

2fhj__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Crystal structure of formylmethanofuran: tetrahydromethanopterin formyltransferase in complex with its coenzymes

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

Formylmethanofuran--tetrahydromethanopterin formyltransferase

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

2fhj__assembly_1__model_1

2fhj__assembly_1__model_1 | I(q)

2fhj__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)