SAXSdb — 2d4h

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

Interferon-induced guanylate-binding protein 1

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	GUANOSINE-5'-MONOPHOSPHATE × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	GUANOSINE-5'-MONOPHOSPHATE × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GBP1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 12–328； UniProt 1–317 Author chain B； PDBConstruct 12–328； UniProt 1–317

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	2d4h
Deposition date deposition_date	2005-10-19
Structure title title	Crystal-structure of the N-terminal large GTPase Domain of human Guanylate Binding protein 1 (hGBP1) in complex with GMP
Keywords keywords	Protein- guanine nucleotide complex, SIGNALING PROTEIN; SIGNALING PROTEIN
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.

2d4h__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2d4h__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2d4h__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	20.30 Å
Rg (electron density)	19.02 Å
Total Rg	20.05 Å
Atom count	2269
Residues	284
Excluded volume	40793 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2d4h__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2d4h__assembly_2__model_1`	monomeric （1）	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	Interferon-induced guanylate-binding protein 1
Molecular weight formula_weight	37078.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4778

MHHHHHHMRGSMASEIHMTGPMCLIENTNGRLMANPEALKILSAITQPMVVVAIVGLYRTGKSYLMNKLAGKKKGFSLGSTVQSHTKGIWMWCVPHPKKPGHILVLLDTEGLGDVEKGDNQNDSWIFALAVLLSSTFVYNSIGTINQQAMDQLYYVTELTHRIRSKSSPDENENEVEDSADFVSFFPDFVWTLRDFSLDLEADGQPLTPDEYLTYSLKLKKGTSQKDETFNLPRLCIRKFFPKKKCFVFDRPVHRRKLAQLEKLQDEELDPEFVQQVADFCSYIFSNSKTKTLSGGIQVNGPRLESLVLTYVNAISSGDLPCMENAVL

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21

Entity 2 Entity 2 non-polymer

Description description	GUANOSINE-5'-MONOPHOSPHATE
Molecular weight formula_weight	363.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	119

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2d4ha1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.8 — G proteins

Domain ID domain_id	d2d4ha2
Class class	a — All alpha proteins
Fold Fold fold	a.114 — Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
Superfamily Superfamily superfamily	a.114.1 — Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
Family Family family	a.114.1.0 — automated matches

Domain ID domain_id	d2d4hb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.8 — G proteins

Domain ID domain_id	d2d4hb2
Class class	a — All alpha proteins
Fold Fold fold	a.114 — Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
Superfamily Superfamily superfamily	a.114.1 — Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
Family Family family	a.114.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	2d4hA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	2d4hB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

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Unit-cell length a length_a	39.921 Å
Unit-cell length b length_b	173.450 Å
Unit-cell length c length_c	49.632 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	110.85 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	19.920 Å
R factor r_factor	0.2350
R_work r_work	0.2330
R_free r_free	0.2750

Crystal-structure of the N-terminal large GTPase Domain of human Guanylate Binding protein 1 (hGBP1) in complex with GMP

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

Interferon-induced guanylate-binding protein 1

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

2d4h__assembly_2__model_1

2d4h__assembly_2__model_1 | I(q)

2d4h__assembly_2__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) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

7. Citations (3)

Crystal-structure of the N-terminal large GTPase Domain of human Guanylate Binding protein 1 (hGBP1) in complex with GMP

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

Interferon-induced guanylate-binding protein 1

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

2d4h__assembly_2__model_1

2d4h__assembly_2__model_1 | I(q)

2d4h__assembly_2__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) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

7. Citations (3)