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6d4g

N-GTPase domain of p190RhoGAP-A

Method: X-RAY DIFFRACTION Dmax: 87.3 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Rho GTPase-activating protein 35

Rattus norvegicus

UniProt P81128

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 1–266 Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；25% (w/v) PEG 8000, 100 mM Tris pH 8.5 Resolution 2.80 Å R-free 0.290
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 1–266 Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；25% (w/v) PEG 8000, 100 mM Tris pH 8.5 Resolution 2.80 Å R-free 0.290

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 6D4G Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5IRC p190A GAP domain complex with RhoA Deposited 2016-03-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1242–1439（198 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) CL CHLORIDE ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 MGF TRIFLUOROMAGNESATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；294 K；30% PEG 2000MME 150mM KCSN 100mM MES, pH 6.5
Resolution 1.72 Å R-free 0.213
5IRC p190A GAP domain complex with RhoA Deposited 2016-03-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1242–1439（198 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) CL CHLORIDE ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 MGF TRIFLUOROMAGNESATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；294 K；30% PEG 2000MME 150mM KCSN 100mM MES, pH 6.5
Resolution 1.72 Å R-free 0.213
5IRC p190A GAP domain complex with RhoA Deposited 2016-03-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1242–1439（198 aa）
Chain B 1242–1439（198 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) CL CHLORIDE ION × 3 GDP GUANOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 2 MGF TRIFLUOROMAGNESATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；294 K；30% PEG 2000MME 150mM KCSN 100mM MES, pH 6.5
Resolution 1.72 Å R-free 0.213

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

View Construct and Data Evidence
UniProt name RHG35_RAT
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 6–271； UniProt 1–266 Author chain B； PDBConstruct 6–271； UniProt 1–266

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 6d4g

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6d4g
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6d4g
Deposition date deposition_date2018-04-18
Structure title titleN-GTPase domain of p190RhoGAP-A
Keywords keywordsGTPase, pseudoGTPase, GTP, p190RhoGAP, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier24.89 Å
Radius of gyration Rg (electron density) rg_electron24.47 Å
Forward intensity I(0) i041364000.00
Molecular weight molecular_weight48176.0 kDa
Excluded volume excluded_volume59671 ų
Envelope volume envelope_volume73475 ų
Hydration-shell volume shell_volume25502 ų
Envelope diameter envelope_diameter84.6 Å
Shell Rg shell_rg31.12 Å
Envelope Rg envelope_rg24.47 Å
Shape Rg shape_rg24.47 Å
Total Rg total_rg25.24 Å
Total atoms total_atoms3374
Residues n_residues418
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 dmax87.3 Å
Rg (real space) rg_real26.01 Å
Rg uncertainty (real space) rg_real_error0.29 Å
I(0) (real space) i0_real4.1410e+07
I(0) uncertainty (real space) i0_real_error5.1440e+05
Rg (reciprocal space) rg_reciprocal24.91 Å
I(0) (reciprocal space) i0_reciprocal41360000.0000
Solution quality estimate total_estimate0.6486
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary26.3 Å
Skewness Skewness skewness0.494
Kurtosis Kurtosis kurtosis-0.193
Angular range angular_range— – 0.3200 Å−1
Current regularization parameter α current_alpha4.7300
Highest regularization parameter α highest_alpha9747000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.805; Stabil: 0.882; Sysdev: 0.000; Positv: 1.000; Valcen: 0.857; Smooth: 0.564
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id6d4gA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id6d4gB00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
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8. Citations (1)

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9. Files and Curves (10)