7y08

Crystal structure of Ricin A chain bound with (2-amino-4-oxo-3,4-dihydropteridine-7-carbonyl)glycyl-L-phenylalanine

Method: X-RAY DIFFRACTION Dmax: 67.0 Å Quality: REASONABLE

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

Ricin A chain

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 RS8 N-[(2-amino-4-oxo-1,4-dihydropteridin-7-yl)carbonyl]glycyl-L-phenylalanine × 1 SO4 SULFATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5;296 K;Ammonium sulfate, Sodium malonate Resolution 1.25 Å R-free 0.253

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 8–274; 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 7y08

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7y08
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7y08
Deposition date deposition_date2022-06-03
Structure title titleCrystal structure of Ricin A chain bound with (2-amino-4-oxo-3,4-dihydropteridine-7-carbonyl)glycyl-L-phenylalanine
Keywords keywordsHYDROLASE INHIBITOR, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier19.49
Radius of gyration Rg (electron density) rg_electron18.22
Forward intensity I(0) i015934000.00
Molecular weight molecular_weight29665.0 kDa
Excluded volume excluded_volume36906 ų
Envelope volume envelope_volume42863 ų
Hydration-shell volume shell_volume19402 ų
Envelope diameter envelope_diameter71.8
Shell Rg shell_rg24.84
Envelope Rg envelope_rg18.84
Shape Rg shape_rg18.23
Total Rg total_rg19.13
Total atoms total_atoms2094
Residues n_residues262
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 dmax67.0
Rg (real space) rg_real19.39
Rg uncertainty (real space) rg_real_error0.36
I(0) (real space) i0_real1.5930e+07
I(0) uncertainty (real space) i0_real_error2.0310e+05
Rg (reciprocal space) rg_reciprocal19.41
I(0) (reciprocal space) i0_reciprocal15930000.0000
Solution quality estimate total_estimate0.6300
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary24.5
Skewness Skewness skewness0.250
Kurtosis Kurtosis kurtosis-0.191
Angular range angular_range— – 0.4100 −1
Current regularization parameter α current_alpha0.0002
Highest regularization parameter α highest_alpha4319000.0000
Real-space data points n_real_points72
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.731; Stabil: 1.000; Sysdev: 0.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.999

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id7y08A01
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

8. Citations (1)

9. Files and Curves (10)