1i4l

CRYSTAL STRUCTURE ANALYSIS OF RAC1-GDP IN COMPLEX WITH ARFAPTIN (P41)

Method: X-RAY DIFFRACTION Dmax: 83.3 Å Quality: REASONABLE

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

ARFAPTIN 2

Homo sapiens

UniProt P53365

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain A; UniProt 118–341 Chain B; UniProt 118–341 Fragment:RESIDUES 118-341 RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 1 × 1 (P63000) MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 9;291 K;Tris, PEG20K, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 2.70 Å R-free 0.301
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain A; UniProt 118–341 Chain B; UniProt 118–341 Fragment:RESIDUES 118-341 RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 1 × 1 (P63000) MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 9;291 K;Tris, PEG20K, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 2.70 Å R-free 0.301

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.

5 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ARFP2_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–224; UniProt 118–341 Author chain B; PDBConstruct 1–224; UniProt 118–341

RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 1

Homo sapiens

UniProt P63000

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain D; UniProt 1–192 Not recorded ARFAPTIN 2 × 2 (P53365) MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 9;291 K;Tris, PEG20K, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 2.70 Å R-free 0.301
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain D; UniProt 1–192 Not recorded ARFAPTIN 2 × 2 (P53365) MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 9;291 K;Tris, PEG20K, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 2.70 Å R-free 0.301

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.

74 other PDB entries and 101 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RAC1_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain D; PDBConstruct 1–192; UniProt 1–192

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 1i4l

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1i4l
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1i4l
Deposition date deposition_date2001-02-22
Structure title titleCRYSTAL STRUCTURE ANALYSIS OF RAC1-GDP IN COMPLEX WITH ARFAPTIN (P41)
Keywords keywordscoiled coil, GTPase, complex, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier31.44
Radius of gyration Rg (electron density) rg_electron31.57
Forward intensity I(0) i059367900.00
Molecular weight molecular_weight61463.0 kDa
Excluded volume excluded_volume77410 ų
Envelope volume envelope_volume102930 ų
Hydration-shell volume shell_volume29766 ų
Envelope diameter envelope_diameter150.5
Shell Rg shell_rg34.48
Envelope Rg envelope_rg33.28
Shape Rg shape_rg31.59
Total Rg total_rg31.81
Total atoms total_atoms4323
Residues n_residues540
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 dmax83.3
Rg (real space) rg_real29.07
Rg uncertainty (real space) rg_real_error0.20
I(0) (real space) i0_real5.6280e+07
I(0) uncertainty (real space) i0_real_error6.5120e+05
Rg (reciprocal space) rg_reciprocal31.73
I(0) (reciprocal space) i0_reciprocal59360000.0000
Solution quality estimate total_estimate0.6869
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary33.3
Skewness Skewness skewness0.294
Kurtosis Kurtosis kurtosis-0.537
Angular range angular_range— – 0.2500 −1
Current regularization parameter α current_alpha1.7590
Highest regularization parameter α highest_alpha8316000.0000
Real-space data points n_real_points51
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.997; Stabil: 0.984; Sysdev: 0.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd1i4la_
Class classa — All alpha proteins
Fold Fold folda.238 — BAR/IMD domain-like
Superfamily Superfamily superfamilya.238.1 — BAR/IMD domain-like
Family Family familya.238.1.2 — Arfaptin, Rac-binding fragment
Domain ID domain_idd1i4lb_
Class classa — All alpha proteins
Fold Fold folda.238 — BAR/IMD domain-like
Superfamily Superfamily superfamilya.238.1 — BAR/IMD domain-like
Family Family familya.238.1.2 — Arfaptin, Rac-binding fragment
Domain ID domain_idd1i4ld_
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 (3 domains)

Domain ID domain_id1i4lA00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
Homologous superfamily homologous superfamily60 — Arfaptin homology (AH) domain/BAR domain
Domain ID domain_id1i4lB00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
Homologous superfamily homologous superfamily60 — Arfaptin homology (AH) domain/BAR domain
Domain ID domain_id1i4lD00
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)