6ury

Crystal structure of ricin A chain in complex with inhibitor 9-oxo-4-fluorenecarboxamide

Method: X-RAY DIFFRACTION Dmax: 100.7 Å Quality: REASONABLE

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 R6T 9-oxo-9H-fluorene-4-carboxamide × 1 EDO 1,2-ETHANEDIOL × 17 CL CHLORIDE ION × 10 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7;295 K;100 mM Tris pH 7.0, 200 mM Magnesium Chloride, 2.5 M Sodium Chloride Resolution 1.54 Å R-free 0.195
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 36–302 Not recorded EDO 1,2-ETHANEDIOL × 4 CL CHLORIDE ION × 6 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7;295 K;100 mM Tris pH 7.0, 200 mM Magnesium Chloride, 2.5 M Sodium Chloride Resolution 1.54 Å R-free 0.195

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 125 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 Author chain B; 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 6ury

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id6ury
Deposition date deposition_date2019-10-24
Structure title titleCrystal structure of ricin A chain in complex with inhibitor 9-oxo-4-fluorenecarboxamide
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_guinier27.37
Radius of gyration Rg (electron density) rg_electron26.60
Forward intensity I(0) i062147400.00
Molecular weight molecular_weight60945.0 kDa
Excluded volume excluded_volume76037 ų
Envelope volume envelope_volume94704 ų
Hydration-shell volume shell_volume29958 ų
Envelope diameter envelope_diameter105.7
Shell Rg shell_rg33.44
Envelope Rg envelope_rg27.11
Shape Rg shape_rg26.60
Total Rg total_rg27.32
Total atoms total_atoms4275
Residues n_residues528
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 dmax100.7
Rg (real space) rg_real27.42
Rg uncertainty (real space) rg_real_error0.98
I(0) (real space) i0_real6.2150e+07
I(0) uncertainty (real space) i0_real_error9.3940e+05
Rg (reciprocal space) rg_reciprocal27.41
I(0) (reciprocal space) i0_reciprocal62150000.0000
Solution quality estimate total_estimate0.5849
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary29.5
Skewness Skewness skewness0.426
Kurtosis Kurtosis kurtosis-0.240
Angular range angular_range— – 0.2900 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha14350000.0000
Real-space data points n_real_points59
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.632; Stabil: 0.997; Sysdev: 0.267; Positv: 1.000; Valcen: 0.912; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd6urya1
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
Domain ID domain_idd6urya2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd6uryb_
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 (4 domains)

Domain ID domain_id6uryA01
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_id6uryA02
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology470 — Ricin (A Subunit), domain 2
Homologous superfamily homologous superfamily10 — Ricin (A Subunit), domain 2
Domain ID domain_id6uryB01
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_id6uryB02
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)