1n3t

Biosynthesis of pteridins. Reaction mechanism of GTP cyclohydrolase I

Method: X-RAY DIFFRACTION

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

GTP cyclohydrolase I

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 10	GUANOSINE-5'-TRIPHOSPHATE × 10	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 10	GUANOSINE-5'-TRIPHOSPHATE × 10	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GCH1_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–221； UniProt 1–221 Author chain B； PDBConstruct 1–221； UniProt 1–221 Author chain C； PDBConstruct 1–221； UniProt 1–221 Author chain D； PDBConstruct 1–221； UniProt 1–221 Author chain E； PDBConstruct 1–221； UniProt 1–221 Author chain F； PDBConstruct 1–221； UniProt 1–221 Author chain G； PDBConstruct 1–221； UniProt 1–221 Author chain H； PDBConstruct 1–221； UniProt 1–221 Author chain I； PDBConstruct 1–221； UniProt 1–221 Author chain J； PDBConstruct 1–221； UniProt 1–221 Author chain K； PDBConstruct 1–221； UniProt 1–221 Author chain L； PDBConstruct 1–221； UniProt 1–221 Author chain M； PDBConstruct 1–221； UniProt 1–221 Author chain N； PDBConstruct 1–221； UniProt 1–221 Author chain O； PDBConstruct 1–221； UniProt 1–221

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	1n3t
Deposition date deposition_date	2002-10-29
Structure title title	Biosynthesis of pteridins. Reaction mechanism of GTP cyclohydrolase I
Keywords keywords	Biosynthesis, folic acid, GTP cyclohydrolase I, tetrahydropterin, pteridines, HYDROLASE; HYDROLASE
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.

1n3t__assembly_1__model_1

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

Download this curve (.dat)

1n3t__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1n3t__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	38.20 Å
Rg (electron density)	37.47 Å
Total Rg	38.05 Å
Atom count	17650
Residues	2210
Excluded volume	313470 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1n3t__assembly_1__model_1`	decameric （10）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1n3t__assembly_2__model_1`	decameric （10）	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 (2)

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6. Fold Classification (SCOP + CATH) 45 domains

SCOP 2.08 (15 domains)

Domain ID domain_id	d1n3ta_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.96 — T-fold
Superfamily Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
Family Family family	d.96.1.1 — GTP cyclohydrolase I

Domain ID domain_id	d1n3tb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.96 — T-fold
Superfamily Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
Family Family family	d.96.1.1 — GTP cyclohydrolase I

Domain ID domain_id	d1n3tc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.96 — T-fold
Superfamily Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
Family Family family	d.96.1.1 — GTP cyclohydrolase I

Domain ID domain_id	d1n3td_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.96 — T-fold
Superfamily Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
Family Family family	d.96.1.1 — GTP cyclohydrolase I

Domain ID domain_id	d1n3te_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.96 — T-fold
Superfamily Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
Family Family family	d.96.1.1 — GTP cyclohydrolase I

Domain ID domain_id	d1n3tf_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.96 — T-fold
Superfamily Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
Family Family family	d.96.1.1 — GTP cyclohydrolase I

Domain ID domain_id	d1n3tg_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.96 — T-fold
Superfamily Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
Family Family family	d.96.1.1 — GTP cyclohydrolase I

Domain ID domain_id	d1n3th_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.96 — T-fold
Superfamily Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
Family Family family	d.96.1.1 — GTP cyclohydrolase I

Domain ID domain_id	d1n3ti_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.96 — T-fold
Superfamily Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
Family Family family	d.96.1.1 — GTP cyclohydrolase I

Domain ID domain_id	d1n3tj_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.96 — T-fold
Superfamily Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
Family Family family	d.96.1.1 — GTP cyclohydrolase I

Domain ID domain_id	d1n3tk_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.96 — T-fold
Superfamily Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
Family Family family	d.96.1.1 — GTP cyclohydrolase I

Domain ID domain_id	d1n3tl_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.96 — T-fold
Superfamily Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
Family Family family	d.96.1.1 — GTP cyclohydrolase I

Domain ID domain_id	d1n3tm_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.96 — T-fold
Superfamily Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
Family Family family	d.96.1.1 — GTP cyclohydrolase I

Domain ID domain_id	d1n3tn_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.96 — T-fold
Superfamily Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
Family Family family	d.96.1.1 — GTP cyclohydrolase I

Domain ID domain_id	d1n3to_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.96 — T-fold
Superfamily Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
Family Family family	d.96.1.1 — GTP cyclohydrolase I

CATH v4.4 (30 domains)

Domain ID domain_id	1n3tA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	286 — GTP Cyclohydrolase I; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — GTP cyclohydrolase I, N-terminal domain

Domain ID domain_id	1n3tA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1130 — GTP Cyclohydrolase I, domain 2
Homologous superfamily homologous superfamily	10 — GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain

Domain ID domain_id	1n3tB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	286 — GTP Cyclohydrolase I; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — GTP cyclohydrolase I, N-terminal domain

Domain ID domain_id	1n3tB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1130 — GTP Cyclohydrolase I, domain 2
Homologous superfamily homologous superfamily	10 — GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain

Domain ID domain_id	1n3tC01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	286 — GTP Cyclohydrolase I; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — GTP cyclohydrolase I, N-terminal domain

Domain ID domain_id	1n3tC02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1130 — GTP Cyclohydrolase I, domain 2
Homologous superfamily homologous superfamily	10 — GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain

Domain ID domain_id	1n3tD01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	286 — GTP Cyclohydrolase I; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — GTP cyclohydrolase I, N-terminal domain

Domain ID domain_id	1n3tD02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1130 — GTP Cyclohydrolase I, domain 2
Homologous superfamily homologous superfamily	10 — GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain

Domain ID domain_id	1n3tE01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	286 — GTP Cyclohydrolase I; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — GTP cyclohydrolase I, N-terminal domain

Domain ID domain_id	1n3tE02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1130 — GTP Cyclohydrolase I, domain 2
Homologous superfamily homologous superfamily	10 — GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain

Domain ID domain_id	1n3tF01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	286 — GTP Cyclohydrolase I; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — GTP cyclohydrolase I, N-terminal domain

Domain ID domain_id	1n3tF02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1130 — GTP Cyclohydrolase I, domain 2
Homologous superfamily homologous superfamily	10 — GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain

Domain ID domain_id	1n3tG01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	286 — GTP Cyclohydrolase I; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — GTP cyclohydrolase I, N-terminal domain

Domain ID domain_id	1n3tG02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1130 — GTP Cyclohydrolase I, domain 2
Homologous superfamily homologous superfamily	10 — GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain

Domain ID domain_id	1n3tH01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	286 — GTP Cyclohydrolase I; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — GTP cyclohydrolase I, N-terminal domain

Domain ID domain_id	1n3tH02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1130 — GTP Cyclohydrolase I, domain 2
Homologous superfamily homologous superfamily	10 — GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain

Domain ID domain_id	1n3tI01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	286 — GTP Cyclohydrolase I; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — GTP cyclohydrolase I, N-terminal domain

Domain ID domain_id	1n3tI02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1130 — GTP Cyclohydrolase I, domain 2
Homologous superfamily homologous superfamily	10 — GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain

Domain ID domain_id	1n3tJ01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	286 — GTP Cyclohydrolase I; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — GTP cyclohydrolase I, N-terminal domain

Domain ID domain_id	1n3tJ02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1130 — GTP Cyclohydrolase I, domain 2
Homologous superfamily homologous superfamily	10 — GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain

Domain ID domain_id	1n3tK01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	286 — GTP Cyclohydrolase I; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — GTP cyclohydrolase I, N-terminal domain

Domain ID domain_id	1n3tK02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1130 — GTP Cyclohydrolase I, domain 2
Homologous superfamily homologous superfamily	10 — GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain

Domain ID domain_id	1n3tL01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	286 — GTP Cyclohydrolase I; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — GTP cyclohydrolase I, N-terminal domain

Domain ID domain_id	1n3tL02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1130 — GTP Cyclohydrolase I, domain 2
Homologous superfamily homologous superfamily	10 — GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain

Domain ID domain_id	1n3tM01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	286 — GTP Cyclohydrolase I; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — GTP cyclohydrolase I, N-terminal domain

Domain ID domain_id	1n3tM02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1130 — GTP Cyclohydrolase I, domain 2
Homologous superfamily homologous superfamily	10 — GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain

Domain ID domain_id	1n3tN01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	286 — GTP Cyclohydrolase I; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — GTP cyclohydrolase I, N-terminal domain

Domain ID domain_id	1n3tN02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1130 — GTP Cyclohydrolase I, domain 2
Homologous superfamily homologous superfamily	10 — GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain

Domain ID domain_id	1n3tO01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	286 — GTP Cyclohydrolase I; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — GTP cyclohydrolase I, N-terminal domain

Domain ID domain_id	1n3tO02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1130 — GTP Cyclohydrolase I, domain 2
Homologous superfamily homologous superfamily	10 — GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain

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Unit-cell length a length_a	223.140 Å
Unit-cell length b length_b	317.810 Å
Unit-cell length c length_c	132.150 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	120

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	3.200 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1850
R_work r_work	0.1850
R_free r_free	0.2280

Description description	GTP cyclohydrolase I
Molecular weight formula_weight	24717.4 kDa
EC 编号 ec_number	3.5.4.16
Mutation mutation	C181S
Source method src_method	man
Copy count entity_count	15

Polymer type type	polypeptide(L)
Chain IDs strand_id	F,G,H,I,J,K,L,M,N,O,A,B,C,D,E
Atom count atom_count	26475

Biosynthesis of pteridins. Reaction mechanism of GTP cyclohydrolase I

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

GTP cyclohydrolase I

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

1n3t__assembly_1__model_1

1n3t__assembly_1__model_1 | I(q)

1n3t__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

6. Fold Classification (SCOP + CATH) 45 domains

SCOP 2.08 (15 domains)

CATH v4.4 (30 domains)

7. Citations (1)

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Description description	GUANOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	523.2 kDa
Source method src_method	syn
Copy count entity_count	15

Biosynthesis of pteridins. Reaction mechanism of GTP cyclohydrolase I

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

GTP cyclohydrolase I

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

1n3t__assembly_1__model_1

1n3t__assembly_1__model_1 | I(q)

1n3t__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

6. Fold Classification (SCOP + CATH) 45 domains

SCOP 2.08 (15 domains)

CATH v4.4 (30 domains)

7. Citations (1)