8dt4

X-ray structure of human acetylcholinesterase ternary complex with paraoxon and oxime MMB4 (POX-hAChE-MMB4)

Method: X-RAY DIFFRACTION Dmax: 104.6 Å Quality: EXCELLENT

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

Acetylcholinesterase

Homo sapiens

UniProt P22303

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 32–578 Chain B; UniProt 32–578 Not recorded DEP DIETHYL PHOSPHONATE × 2 3VI 1,1'-methylenebis{4-[(E)-(hydroxyimino)methyl]pyridin-1-ium} × 2 GOL GLYCEROL × 6 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.5;283 K;100 mM HEPES, pH 7.5, 100 mM KNO3 and 9 % PEG3350 Resolution 2.80 Å R-free 0.220

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.

77 other PDB entries and 84 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ACES_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 4–550; UniProt 32–578 Author chain B; PDBConstruct 4–550; UniProt 32–578

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 8dt4

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8dt4
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8dt4
Deposition date deposition_date2022-07-25
Structure title titleX-ray structure of human acetylcholinesterase ternary complex with paraoxon and oxime MMB4 (POX-hAChE-MMB4)
Keywords keywordsacetylcholine hydrolysis, oxime reactivator, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier33.21
Radius of gyration Rg (electron density) rg_electron32.36
Forward intensity I(0) i0217749000.00
Molecular weight molecular_weight119650.0 kDa
Excluded volume excluded_volume150060 ų
Envelope volume envelope_volume182470 ų
Hydration-shell volume shell_volume45449 ų
Envelope diameter envelope_diameter111.4
Shell Rg shell_rg40.41
Envelope Rg envelope_rg32.33
Shape Rg shape_rg32.34
Total Rg total_rg33.05
Total atoms total_atoms8466
Residues n_residues1080
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 dmax104.6
Rg (real space) rg_real33.14
Rg uncertainty (real space) rg_real_error0.68
I(0) (real space) i0_real2.1770e+08
I(0) uncertainty (real space) i0_real_error3.5610e+06
Rg (reciprocal space) rg_reciprocal33.17
I(0) (reciprocal space) i0_reciprocal217800000.0000
Solution quality estimate total_estimate0.9043
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary37.0
Skewness Skewness skewness0.264
Kurtosis Kurtosis kurtosis-0.545
Angular range angular_range— – 0.2400 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha66990000.0000
Real-space data points n_real_points49
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.939; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.936

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id8dt4A01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1820 — Alpha/Beta hydrolase fold, catalytic domain
Domain ID domain_id8dt4B01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1820 — Alpha/Beta hydrolase fold, catalytic domain

8. Citations (1)

9. Files and Curves (10)