SAXSdb — 6k2d

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

Guanylate-binding protein 1

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–479	Not recorded	E3 ubiquitin-protein ligase ipaH9.8 × 1 （Q8VSC3）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；291 K；1.6M Sodium/potassium phosphate pH 6.5	Resolution 3.60 Å R-free 0.287

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 6K2D	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1DG3 STRUCTURE OF HUMAN GUANYLATE BINDING PROTEIN-1 IN NUCLEOTIDE FREE FORM Deposited 1999-11-23	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–592（592 aa） Fragment：FULL LENGTH PROTEIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；100MM MES-NAOH, 7.5% PEG6000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.80 Å R-free 0.276
1F5N HUMAN GUANYLATE BINDING PROTEIN-1 IN COMPLEX WITH THE GTP ANALOGUE, GMPPNP. Deposited 2000-06-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–592（592 aa）	Mutation：Q507H	MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；15-20% PEG3350, 150-200mM MgCl2, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 4K	Resolution 1.70 Å R-free 0.255
2B8W Crystal-structure of the N-terminal Large GTPase Domain of human Guanylate Binding protein 1 (hGBP1) in complex with GMP/AlF4 Deposited 2005-10-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–317（317 aa） Fragment：N-terminal Large GTPase domain Chain B 1–317（317 aa） Fragment：N-terminal Large GTPase domain	Not recorded	MG MAGNESIUM ION × 2 ALF TETRAFLUOROALUMINATE ION × 2 5GP GUANOSINE-5'-MONOPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions 298 K；5% PEG3350, 150 mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.22 Å R-free 0.233
2B92 Crystal-structure of the N-terminal Large GTPase Domain of human Guanylate Binding protein 1 (hGBP1) in complex with GDP/AlF3 Deposited 2005-10-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–317（317 aa） Fragment：N-terminal Large GTPase domain Chain B 1–317（317 aa） Fragment：N-terminal Large GTPase domain	Not recorded	MG MAGNESIUM ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 2 AF3 ALUMINUM FLUORIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions 298 K；12.5% Peg3350, 125mM Na2HPO4 (from Hampton Research peg/ion screen supplied at pH9.1), VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.20 Å R-free 0.250
2BC9 Crystal-structure of the N-terminal large GTPase Domain of human Guanylate Binding protein 1 (hGBP1) in complex with non-hydrolysable GTP analogue GppNHp Deposited 2005-10-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–317（317 aa） Fragment：N-terminal Large GTPase doamin	Not recorded	MG MAGNESIUM ION × 2 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；10 % Peg 3350, 100 mM NaSCN, 40 mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.80 Å R-free 0.269
2D4H Crystal-structure of the N-terminal large GTPase Domain of human Guanylate Binding protein 1 (hGBP1) in complex with GMP Deposited 2005-10-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–317（317 aa） Fragment：N-terminal Large GTPase domain	Not recorded	5GP GUANOSINE-5'-MONOPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions 298 K；20% Peg 3350, 130 mM NH4NO3, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.90 Å R-free 0.275
2D4H Crystal-structure of the N-terminal large GTPase Domain of human Guanylate Binding protein 1 (hGBP1) in complex with GMP Deposited 2005-10-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–317（317 aa） Fragment：N-terminal Large GTPase domain	Not recorded	5GP GUANOSINE-5'-MONOPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions 298 K；20% Peg 3350, 130 mM NH4NO3, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.90 Å R-free 0.275
6K1Z Crystal structure of farnesylated hGBP1 Deposited 2019-05-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–592（592 aa）	Not recorded	FAR FARNESYL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；0.02M Citric acid/0.08M BIS-TRIS propane (pH 8.8), 16% w/v Polyethylene glycol 3350	Resolution 2.31 Å R-free 0.267
6LOJ The complex structure of IpaH9.8-LRR and hGBP1 Deposited 2020-01-06	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–592（592 aa）	Mutation：Q507H	GDP GUANOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；2.5M NaCl, 0.1M K/Na phosphate buffer, pH 6	Resolution 3.72 Å R-free 0.256
8CQB Cryo-EM structure of the human GBP1 dimer bound to GDP-AlF3 Deposited 2023-03-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–592（592 aa） Chain B 1–592（592 aa）	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 2 AF3 ALUMINUM FLUORIDE × 2 MG MAGNESIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；5u mM HEPES pH7.4, 150 mM NaCl, 1 mM DTT, 200 uM GDP, 10 mM NaF, 300 uM AlCl3, 5 mM MgCl2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
8Q4L GBP1 bound by 14-3-3sigma Deposited 2023-08-07	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 7–583（577 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8；150 mM KCl, 20 mM HEPES-KOH pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.12 Å

10 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	GBP1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–481； UniProt 1–479

E3 ubiquitin-protein ligase ipaH9.8

Shigella flexneri

UniProt Q8VSC3

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 22–252	Fragment：LRR domain	Guanylate-binding protein 1 × 1 （P32455）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；291 K；1.6M Sodium/potassium phosphate pH 6.5	Resolution 3.60 Å R-free 0.287

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 6K2D	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5B0N Structure of Shigella effector LRR domain Deposited 2015-11-02	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–244（223 aa） Fragment：UNP residues 22-244	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；0.1M BIS-TRIS pH5.5, 0.2M Lithium Sulfate monohydrate, 25% (w/v) PEG3350	Resolution 1.80 Å R-free 0.259
5B0N Structure of Shigella effector LRR domain Deposited 2015-11-02	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 22–244（223 aa） Fragment：UNP residues 22-244	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；0.1M BIS-TRIS pH5.5, 0.2M Lithium Sulfate monohydrate, 25% (w/v) PEG3350	Resolution 1.80 Å R-free 0.259
5B0T Structure of Shigella effector LRR domain Deposited 2015-11-04	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–244（223 aa） Fragment：UNP residues 21-244	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；0.1M BIS-TRIS pH5.5, 0.2M Ammonium Sulfate, 25% (w/v) PEG3350	Resolution 2.00 Å R-free 0.265

2 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	IPA9_SHIFL
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 6–236； UniProt 22–252

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	6k2d
Deposition date deposition_date	2019-05-14
Structure title title	The crystal structure of GBP1 with LRR domain of IpaH9.8
Keywords keywords	Complex, HYDROLASE-TRANSFERASE complex; HYDROLASE/TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	37.91 Å
Radius of gyration Rg (electron density) rg_electron	39.13 Å
Forward intensity I(0) i0	81449700.00
Molecular weight molecular_weight	72944.0 kDa
Excluded volume excluded_volume	91870 Å³
Envelope volume envelope_volume	130720 Å³
Hydration-shell volume shell_volume	32651 Å³
Envelope diameter envelope_diameter	151.0 Å
Shell Rg shell_rg	38.07 Å
Envelope Rg envelope_rg	40.07 Å
Shape Rg shape_rg	39.14 Å
Total Rg total_rg	39.03 Å
Total atoms total_atoms	5138
Residues n_residues	642
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	145.1 Å
Rg (real space) rg_real	39.05 Å
Rg uncertainty (real space) rg_real_error	1.84 Å
I(0) (real space) i0_real	8.1450e+07
I(0) uncertainty (real space) i0_real_error	1.3630e+06
Rg (reciprocal space) rg_reciprocal	38.34 Å
I(0) (reciprocal space) i0_reciprocal	81390000.0000
Solution quality estimate total_estimate	0.6741
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	31.1 Å
Skewness Skewness skewness	0.854
Kurtosis Kurtosis kurtosis	0.061
Angular range angular_range	— – 0.2100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	11150000.0000
Real-space data points n_real_points	43
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.245; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.248; Smooth: 0.774

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Guanylate-binding protein 1
Molecular weight formula_weight	54577.1 kDa
EC 编号 ec_number	3.6.5.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	5138

SEMASEIHMTGPMCLIENTNGRLMANPEALKILSAITQPMVVVAIVGLYRTGKSYLMNKLAGKKKGFSLGSTVQSHTKGIWMWCVPHPKKPGHILVLLDTEGLGDVEKGDNQNDSWIFALAVLLSSTFVYNSIGTINQQAMDQLYYVTELTHRIRSKSSPDENENEVEDSADFVSFFPDFVWTLRDFSLDLEADGQPLTPDEYLTYSLKLKKGTSQKDETFNLPRLCIRKFFPKKKCFVFDRPVHRRKLAQLEKLQDEELDPEFVQQVADFCSYIFSNSKTKTLSGGIQVNGPRLESLVLTYVNAISSGDLPCMENAVLALAQIENSAAVQKAIAHYEQQMGQKVQLPTETLQELLDLHRDSEREAIEVFIRSSFKDVDHLFQKELAAQLEKKRDDFCKQNQEASSDRCSALLQVIFSPLEEEVKAGIYSKPGGYRLFVQKLQDLKKKYYEEPRKGIQAEEILQTYLKSKESMTDAILQTD

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	E3 ubiquitin-protein ligase ipaH9.8
Molecular weight formula_weight	26757.1 kDa
EC 编号 ec_number	2.3.2.27
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

SGRPMTYADYFSAWDKWEKQALPGEERDEAVSRLKECLINNSDELRLDRLNLSSLPDNLPAQITLLNVSYNQLTNLPELPVTLKKLYSASNKLSELPVLPPALESLQVQHNELENLPALPDSLLTMNISYNEIVSLPSLPQALKNLRATRNFLTELPAFSEGNNPVVREYFFDRNQISHIPESILNLRNECSIHISDNPLSSHALPALQRLTSSPDYHGPRIYFSMSDGQQNTLHR

来源 Source

来源生物 organism	Shigella flexneri
NCBI Class编号 ncbi_taxonomy_id	623
宿主生物 host_organism	Escherichia coli

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	6k2dA01
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	6k2dB00
Class class	3 — Alpha Beta
Architecture architecture	80 — Alpha-Beta Horseshoe
Topology topology	10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
Homologous superfamily homologous superfamily	10 — Ribonuclease Inhibitor

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8. Citations (1)

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Unit-cell length a length_a	211.736 Å
Unit-cell length b length_b	211.736 Å
Unit-cell length c length_c	56.975 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	3.600 Å
Low-resolution limit resolution_low	48.392 Å
R factor r_factor	0.2429
R_work r_work	0.2404
R_free r_free	0.2872

fit	/app/data/saxs_computation/k2/6k2d/6k2d.fit
pddf	/app/data/pr_computation/k2/6k2d/6k2d.pr.out
profile	/app/data/saxs_computation/k2/6k2d/6k2d.dat

The crystal structure of GBP1 with LRR domain of IpaH9.8

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

Guanylate-binding protein 1

State in the Current Structure

Other States of the Same Protein in the Database

E3 ubiquitin-protein ligase ipaH9.8

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)