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1gdf

STRUCTURE OF RHOGDI: A C-TERMINAL BINDING DOMAIN TARGETS AN N-TERMINAL INHIBITORY PEPTIDE TO GTPASES, NMR, MINIMIZED AVERAGE STRUCTURE

Method: SOLUTION NMR Dmax: 63.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

RHOGDI

Bos taurus

UniProt P19803

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 60–204 Fragment：ISOPRENE BINDING DOMAIN No other associated polymer SOLUTION NMR NMR measurement conditions：pH 6.8；303 K Resolution not provided

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 1GDF Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1AJW STRUCTURE OF RHOGDI: A C-TERMINAL BINDING DOMAIN TARGETS AN N-TERMINAL INHIBITORY PEPTIDE TO GTPASES, NMR, 20 STRUCTURES Deposited 1997-05-11 Parsed fields agree Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 60–204（145 aa） Fragment：ISOPRENE BINDING DOMAIN
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.8；303 K
Resolution not provided
1DOA Structure of the rho family gtp-binding protein cdc42 in complex with the multifunctional regulator rhogdi Deposited 1999-12-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–204（204 aa）
Not recorded MG MAGNESIUM ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 1 GER GERAN-8-YL GERAN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；291 K；15% PEG 4000, 100 mM Glutamic Acid, 25 mM MgSO4, 50 mM Tris, 2 mM NaN3, 2 mM LDAO , pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 18K, temperature 291K
Resolution 2.60 Å R-free 0.320
1DOA Structure of the rho family gtp-binding protein cdc42 in complex with the multifunctional regulator rhogdi Deposited 1999-12-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain B 1–204（204 aa）
Not recorded MG MAGNESIUM ION × 6 GDP GUANOSINE-5'-DIPHOSPHATE × 3 GER GERAN-8-YL GERAN × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；291 K；15% PEG 4000, 100 mM Glutamic Acid, 25 mM MgSO4, 50 mM Tris, 2 mM NaN3, 2 mM LDAO , pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 18K, temperature 291K
Resolution 2.60 Å R-free 0.320
5FR1 Double acetylated RhoGDI-alpha in complex with RhoA-GDP Deposited 2015-12-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–204（204 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.5；4 M SODIUM FORMATE, 0.1 M SODIUM ACETATE PH 4.5
Resolution 2.75 Å R-free 0.256
5FR2 Farnesylated RhoA-GDP in complex with RhoGDI-alpha, lysine acetylated at K178 Deposited 2015-12-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–204（204 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) FAR FARNESYL × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 BGC beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 0.2 M LITHIUMSULFATE 0.1 M BIS-TRIS PH5.5 25% PEG3350 30% DEXTROSE
Resolution 3.35 Å R-free 0.258

4 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GDIR_BOVIN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–145； UniProt 60–204

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.

SAXS scattering curve SAXS Profile

SAXS profile for 1gdf

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1gdf
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1gdf
Deposition date deposition_date1997-05-11
Structure title titleSTRUCTURE OF RHOGDI: A C-TERMINAL BINDING DOMAIN TARGETS AN N-TERMINAL INHIBITORY PEPTIDE TO GTPASES, NMR, MINIMIZED AVERAGE STRUCTURE
Keywords keywordsRHO-GTPASE INHIBITOR, NUCLEOTIDE EXCHANGE, ISOPRENE BINDING; RHO-GTPASE INHIBITOR
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier17.75 Å
Radius of gyration Rg (electron density) rg_electron16.45 Å
Forward intensity I(0) i05383080.00
Molecular weight molecular_weight16684.0 kDa
Excluded volume excluded_volume20962 ų
Envelope volume envelope_volume26158 ų
Hydration-shell volume shell_volume13856 ų
Envelope diameter envelope_diameter66.3 Å
Shell Rg shell_rg21.98 Å
Envelope Rg envelope_rg17.37 Å
Shape Rg shape_rg16.35 Å
Total Rg total_rg17.79 Å
Total atoms total_atoms2346
Residues n_residues145
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax63.4 Å
Rg (real space) rg_real17.79 Å
Rg uncertainty (real space) rg_real_error0.45 Å
I(0) (real space) i0_real5.3830e+06
I(0) uncertainty (real space) i0_real_error6.8520e+04
Rg (reciprocal space) rg_reciprocal17.78 Å
I(0) (reciprocal space) i0_reciprocal5383000.0000
Solution quality estimate total_estimate0.7580
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary20.3 Å
Skewness Skewness skewness0.471
Kurtosis Kurtosis kurtosis0.075
Angular range angular_range— – 0.4500 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1082000.0000
Real-space data points n_real_points76
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.647; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.917; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1gdfa_
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.18 — E set domains
Family Family familyb.1.18.8 — RhoGDI-like

CATH v4.4 (1 domains)

Domain ID domain_id1gdfA00
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology50 — Coagulation Factor XIII; Chain A, domain 1
Homologous superfamily homologous superfamily30 — Coagulation Factor XIII, subunit A, domain 1
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8. Citations (1)

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9. Files and Curves (10)