5irc

p190A GAP domain complex with RhoA

Method: X-RAY DIFFRACTION Dmax: 89.2 Å Quality: EXCELLENT

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 1242–1439 Non-standard monomer:Yes (specific site not provided by mmCIF) Transforming protein RhoA × 1 (P61586) 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
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 1242–1439 Non-standard monomer:Yes (specific site not provided by mmCIF) Transforming protein RhoA × 1 (P61586) 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
3 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 1242–1439 Chain B; UniProt 1242–1439 Non-standard monomer:Yes (specific site not provided by mmCIF) Transforming protein RhoA × 2 (P61586) 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

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.

1 other PDB entries and 2 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 4–201; UniProt 1242–1439 Author chain B; PDBConstruct 4–201; UniProt 1242–1439

Transforming protein RhoA

Homo sapiens

UniProt P61586

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 F; UniProt 2–181 Non-standard monomer:Yes (specific site not provided by mmCIF) Rho GTPase-activating protein 35 × 1 (P81128) 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
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain D; UniProt 2–181 Non-standard monomer:Yes (specific site not provided by mmCIF) Rho GTPase-activating protein 35 × 1 (P81128) 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
3 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain D; UniProt 2–181 Chain F; UniProt 2–181 Non-standard monomer:Yes (specific site not provided by mmCIF) Rho GTPase-activating protein 35 × 2 (P81128) 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

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.

129 other PDB entries and 163 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RHOA_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain D; PDBConstruct 7–186; UniProt 2–181 Author chain F; PDBConstruct 7–186; UniProt 2–181

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 5irc

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5irc
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5irc
Deposition date deposition_date2016-03-12
Structure title titlep190A GAP domain complex with RhoA
Keywords keywordsprotein-protein complex, transition state, GTPase, GAP domain, protein binding; PROTEIN BINDING
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier29.10
Radius of gyration Rg (electron density) rg_electron28.18
Forward intensity I(0) i0115658000.00
Molecular weight molecular_weight84405.0 kDa
Excluded volume excluded_volume105440 ų
Envelope volume envelope_volume129950 ų
Hydration-shell volume shell_volume37615 ų
Envelope diameter envelope_diameter95.4
Shell Rg shell_rg36.23
Envelope Rg envelope_rg27.94
Shape Rg shape_rg28.19
Total Rg total_rg28.97
Total atoms total_atoms5919
Residues n_residues734
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

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

Maximum dimension Dmax dmax89.2
Rg (real space) rg_real28.98
Rg uncertainty (real space) rg_real_error0.50
I(0) (real space) i0_real1.1570e+08
I(0) uncertainty (real space) i0_real_error1.8310e+06
Rg (reciprocal space) rg_reciprocal29.03
I(0) (reciprocal space) i0_reciprocal115700000.0000
Solution quality estimate total_estimate0.9105
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary36.4
Skewness Skewness skewness0.159
Kurtosis Kurtosis kurtosis-0.553
Angular range angular_range— – 0.2700 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha42230000.0000
Real-space data points n_real_points55
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.957; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.966

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (5 domains)

Domain ID domain_idd5irca1
Class classa — All alpha proteins
Fold Fold folda.116 — GTPase activation domain, GAP
Superfamily Superfamily superfamilya.116.1 — GTPase activation domain, GAP
Family Family familya.116.1.0 — automated matches
Domain ID domain_idd5irca2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd5ircb_
Class classa — All alpha proteins
Fold Fold folda.116 — GTPase activation domain, GAP
Superfamily Superfamily superfamilya.116.1 — GTPase activation domain, GAP
Family Family familya.116.1.0 — automated matches
Domain ID domain_idd5ircd_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.8 — G proteins
Domain ID domain_idd5ircf_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.8 — G proteins

CATH v4.4 (4 domains)

Domain ID domain_id5ircA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology555 — Phosphatidylinositol 3-kinase; Chain A
Homologous superfamily homologous superfamily10 — Rho GTPase activation protein
Domain ID domain_id5ircB00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology555 — Phosphatidylinositol 3-kinase; Chain A
Homologous superfamily homologous superfamily10 — Rho GTPase activation protein
Domain ID domain_id5ircD00
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_id5ircF00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases

8. Citations (1)

9. Files and Curves (10)