SAXSdb — 5drv

▼

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

Ras GTPase-activating protein-binding protein 2

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–139	Fragment：NTF2-like domain, UNP residues 1-139	Non-structural protein 3 × 2 （P08411）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.4；293 K；0.9 M tri-sodium citrate, 20 % glycerol, 0.1 M sodium cacodylate (pH 6.4)	Resolution 2.75 Å R-free 0.299

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 5DRV	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9OS2 Cryo-EM structure of the DDB1/CRBN-MRT-5702-G3BP2 ternary complex Deposited 2025-05-23	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–482（482 aa） Chain D 1–482（482 aa）	Not recorded	ZN ZINC ION × 1 A1CED (1S,3S)-2-[(2-chlorophenyl)methanesulfonyl]-N-{[(4R)-3-(2,4-dioxo-1,3-diazinan-1-yl)imidazo[1,2-a]pyridin-7-yl]methyl}-1-methyl-1,2,3,4-tetrahydroisoquinoline-3-carboxamide × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.50 Å

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	G3BP2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–142； UniProt 1–139

Non-structural protein 3

OrganismNot specified

UniProt P08411

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain B； UniProt 1785–1792	Fragment：UNP residues 1785-1792	Ras GTPase-activating protein-binding protein 2 × 2 （Q9UN86）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.4；293 K；0.9 M tri-sodium citrate, 20 % glycerol, 0.1 M sodium cacodylate (pH 6.4)	Resolution 2.75 Å R-free 0.299

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 5DRV	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1FW5 SOLUTION STRUCTURE OF MEMBRANE BINDING PEPTIDE OF SEMLIKI FOREST VIRUS MRNA CAPPING ENZYME NSP1 Deposited 2000-09-21	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 245–264（20 aa） Fragment：RESIDUES 245-364 OF NSP1	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
5FW5 Crystal structure of human G3BP1 in complex with Semliki Forest Virus nsP3-25 comprising two FGDF motives Deposited 2016-02-12	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain C 1785–1809（25 aa） Fragment：RESIDUES 449-473	Not recorded	SO4 SULFATE ION × 8 ACT ACETATE ION × 4 GOL GLYCEROL × 8 K POTASSIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions 0.1 M SODIUM ACETATE TRIHYDRATE PH 4.6, 2 M AMMONIUMSULFATE	Resolution 1.92 Å R-free 0.202

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

View Construct and Data Evidence

UniProt name	POLN_SFV
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–8； UniProt 1785–1792

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	5drv
Deposition date deposition_date	2015-09-16
Structure title title	Crystal structure of the G3BP2 NTF2-like domain in complex with a peptide
Keywords keywords	NTF2-like, G3BP, peptide complex, protein binding; PROTEIN BINDING
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	16.64 Å
Radius of gyration Rg (electron density) rg_electron	15.22 Å
Forward intensity I(0) i0	5096200.00
Molecular weight molecular_weight	15998.0 kDa
Excluded volume excluded_volume	19929 Å³
Envelope volume envelope_volume	24026 Å³
Hydration-shell volume shell_volume	13501 Å³
Envelope diameter envelope_diameter	56.5 Å
Shell Rg shell_rg	21.05 Å
Envelope Rg envelope_rg	15.85 Å
Shape Rg shape_rg	15.15 Å
Total Rg total_rg	16.55 Å
Total atoms total_atoms	1130
Residues n_residues	138
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

▼

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

Maximum dimension Dmax dmax	57.6 Å
Rg (real space) rg_real	16.60 Å
Rg uncertainty (real space) rg_real_error	0.40 Å
I(0) (real space) i0_real	5.0960e+06
I(0) uncertainty (real space) i0_real_error	6.5010e+04
Rg (reciprocal space) rg_reciprocal	16.60 Å
I(0) (reciprocal space) i0_reciprocal	5096000.0000
Solution quality estimate total_estimate	0.8497
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.0 Å
Skewness Skewness skewness	0.360
Kurtosis Kurtosis kurtosis	-0.009
Angular range angular_range	— – 0.4800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1194000.0000
Real-space data points n_real_points	78
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.692; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.970

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Ras GTPase-activating protein-binding protein 2
Molecular weight formula_weight	16138.2 kDa
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	1130

GSHMVMEKPSPLLVGREFVRQYYTLLNKAPEYLHRFYGRNSSYVHGGVDASGKPQEAVYGQNDIHHKVLSLNFSECHTKIRHVDAHATLSDGVVVQVMGLLSNSGQPERKFMQTFVLAPEGSVPNKFYVHNDMFRYEDEVFG

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	Non-structural protein 3
Molecular weight formula_weight	943.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

LTFGDFDE

▼

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	5drvA00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	50 —

▶

8. Citations (1)

▶

Unit-cell length a length_a	94.850 Å
Unit-cell length b length_b	94.850 Å
Unit-cell length c length_c	114.030 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	18

Space group space_group	H 3 2
Space-group number int_tables_number	155
Crystal system crystal_system	—

Resolution resolution	2.750 Å
Low-resolution limit resolution_low	38.641 Å
R factor r_factor	0.2503
R_work r_work	0.2446
R_free r_free	0.2991

fit	/app/data/saxs_computation/dr/5drv/5drv.fit
pddf	/app/data/pr_computation/dr/5drv/5drv.pr.out
profile	/app/data/saxs_computation/dr/5drv/5drv.dat

Crystal structure of the G3BP2 NTF2-like domain in complex with a peptide

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

Ras GTPase-activating protein-binding protein 2

State in the Current Structure

Other States of the Same Protein in the Database

Non-structural protein 3

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

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)