1i4d

CRYSTAL STRUCTURE ANALYSIS OF RAC1-GDP COMPLEXED WITH ARFAPTIN (P21)

Method: X-RAY DIFFRACTION Dmax: 127.7 Å Quality: GOOD

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 2.50 Å R-free 0.298

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 7 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 2.50 Å R-free 0.298

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 102 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 1i4d

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1i4d
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1i4d
Deposition date deposition_date2001-02-20
Structure title titleCRYSTAL STRUCTURE ANALYSIS OF RAC1-GDP COMPLEXED WITH ARFAPTIN (P21)
Keywords keywordscoiled coil, G-protein, 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_guinier31.84
Radius of gyration Rg (electron density) rg_electron31.80
Forward intensity I(0) i062132000.00
Molecular weight molecular_weight62737.0 kDa
Excluded volume excluded_volume78907 ų
Envelope volume envelope_volume103610 ų
Hydration-shell volume shell_volume29890 ų
Envelope diameter envelope_diameter132.8
Shell Rg shell_rg34.57
Envelope Rg envelope_rg32.90
Shape Rg shape_rg31.83
Total Rg total_rg31.96
Total atoms total_atoms4414
Residues n_residues550
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 dmax127.7
Rg (real space) rg_real32.35
Rg uncertainty (real space) rg_real_error1.80
I(0) (real space) i0_real6.2130e+07
I(0) uncertainty (real space) i0_real_error1.1330e+06
Rg (reciprocal space) rg_reciprocal32.13
I(0) (reciprocal space) i0_reciprocal62120000.0000
Solution quality estimate total_estimate0.7594
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary125.1
Skewness Skewness skewness0.761
Kurtosis Kurtosis kurtosis0.599
Angular range angular_range— – 0.2500 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha11240000.0000
Real-space data points n_real_points51
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.471; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.523; Smooth: 0.932

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_idd1i4da_
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_idd1i4db_
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_idd1i4dd_
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_id1i4dA00
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_id1i4dB00
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_id1i4dD00
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)