6urx

Crystal structure of ricin A chain in complex with inhibitor 5-phenyl-2-thiophenecarboxylic acid

Method: X-RAY DIFFRACTION Dmax: 61.2 Å Quality: GOOD

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

Ricin

Ricinus communis

UniProt P02879

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 36–302 Not recorded EDO 1,2-ETHANEDIOL × 15 JMG 5-phenylthiophene-2-carboxylic acid × 1 DMS DIMETHYL SULFOXIDE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;295 K;200 mM Ammonium Iodide, 20% (w/v) PEG 3350 Resolution 1.99 Å R-free 0.218

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.

100 other PDB entries and 126 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RICI_RICCO
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 2–268; UniProt 36–302

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 6urx

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id6urx
Deposition date deposition_date2019-10-24
Structure title titleCrystal structure of ricin A chain in complex with inhibitor 5-phenyl-2-thiophenecarboxylic acid
Keywords keywordsRicin A chain, RTA, Hydrolase, Toxin, Inhibitor, Hydrolase-Hydrolase Inhibitor complex; Hydrolase/Hydrolase Inhibitor
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier19.44
Radius of gyration Rg (electron density) rg_electron18.07
Forward intensity I(0) i016047900.00
Molecular weight molecular_weight30143.0 kDa
Excluded volume excluded_volume37748 ų
Envelope volume envelope_volume43161 ų
Hydration-shell volume shell_volume19592 ų
Envelope diameter envelope_diameter62.5
Shell Rg shell_rg24.66
Envelope Rg envelope_rg18.40
Shape Rg shape_rg18.06
Total Rg total_rg19.05
Total atoms total_atoms2122
Residues n_residues259
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 dmax61.2
Rg (real space) rg_real19.30
Rg uncertainty (real space) rg_real_error0.30
I(0) (real space) i0_real1.6050e+07
I(0) uncertainty (real space) i0_real_error1.7950e+05
Rg (reciprocal space) rg_reciprocal19.33
I(0) (reciprocal space) i0_reciprocal16050000.0000
Solution quality estimate total_estimate0.8946
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary25.9
Skewness Skewness skewness0.136
Kurtosis Kurtosis kurtosis-0.392
Angular range angular_range— – 0.4100 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4442000.0000
Real-space data points n_real_points72
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.878; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.998

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd6urxa_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.165 — Ribosome inactivating proteins (RIP)
Superfamily Superfamily superfamilyd.165.1 — Ribosome inactivating proteins (RIP)
Family Family familyd.165.1.1 — Plant cytotoxins

CATH v4.4 (2 domains)

Domain ID domain_id6urxA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology420 — Ricin (A subunit); domain 1
Homologous superfamily homologous superfamily10 — Ricin (A subunit), domain 1
Domain ID domain_id6urxA02
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology470 — Ricin (A Subunit), domain 2
Homologous superfamily homologous superfamily10 — Ricin (A Subunit), domain 2

8. Citations (1)

9. Files and Curves (10)