5qu9

PanDDA analysis group deposition of ground-state model of Kalirin/Rac1 screened against a customized urea fragment library by X-ray Crystallography at the XChem facility of Diamond Light Source beamline I04-1

Method: X-RAY DIFFRACTION Dmax: 74.0 Å Quality: GOOD

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

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 × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 1–177 Not recorded Kalirin × 1 (O60229) EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5.5;293.15 K;0.1M bis-tris pH 5.5 24% PEG 3350 Resolution 2.00 Å R-free 0.231

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 1
Chains and sequence ranges Author chain A; PDBConstruct 2–178; UniProt 1–177

Kalirin

Homo sapiens

UniProt O60229

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 B; UniProt 1280–1459 Mutation:None Ras-related C3 botulinum toxin substrate 1 × 1 (P63000) EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5.5;293.15 K;0.1M bis-tris pH 5.5 24% PEG 3350 Resolution 2.00 Å R-free 0.231

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.

12 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name KALRN_HUMAN
Isoform O60229-2
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 3–182; UniProt 1280–1459

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 5qu9

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5qu9
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5qu9
Deposition date deposition_date2019-12-13
Structure title titlePanDDA analysis group deposition of ground-state model of Kalirin/Rac1 screened against a customized urea fragment library by X-ray Crystallography at the XChem facility of Diamond Light Source beamline I04-1
Keywords keywordsSGC - Diamond I04-1 fragment screening, XChemExplorer, HYDROLASE-TRANSFERASE complex; HYDROLASE/TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier22.08
Radius of gyration Rg (electron density) rg_electron21.00
Forward intensity I(0) i025273500.00
Molecular weight molecular_weight39450.0 kDa
Excluded volume excluded_volume49786 ų
Envelope volume envelope_volume58783 ų
Hydration-shell volume shell_volume23255 ų
Envelope diameter envelope_diameter73.9
Shell Rg shell_rg27.80
Envelope Rg envelope_rg21.17
Shape Rg shape_rg21.01
Total Rg total_rg21.88
Total atoms total_atoms2777
Residues n_residues356
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 dmax74.0
Rg (real space) rg_real21.95
Rg uncertainty (real space) rg_real_error0.42
I(0) (real space) i0_real2.5270e+07
I(0) uncertainty (real space) i0_real_error3.4800e+05
Rg (reciprocal space) rg_reciprocal21.98
I(0) (reciprocal space) i0_reciprocal25270000.0000
Solution quality estimate total_estimate0.8800
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary27.6
Skewness Skewness skewness0.196
Kurtosis Kurtosis kurtosis-0.380
Angular range angular_range— – 0.3600 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha6452000.0000
Real-space data points n_real_points68
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.821; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.977

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd5qu9a_
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 (2 domains)

Domain ID domain_id5qu9A00
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_id5qu9B00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology900 — Dbl Homology Domain; Chain A
Homologous superfamily homologous superfamily10 — Dbl homology (DH) domain

8. Citations (1)

9. Files and Curves (10)