5fpp

Structure of a pre-reaction ternary complex between sarin- acetylcholinesterase and HI-6

Method: X-RAY DIFFRACTION Dmax: 132.9 Å Quality: GOOD

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

ACETYLCHOLINESTERASE

MUS MUSCULUS

UniProt P21836

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 32–574 Chain B; UniProt 32–574 Fragment:CATALYTIC DOMAIN, UNP RESIDUES 32-574 Non-standard monomer:Yes (specific site not provided by mmCIF) NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CO3 CARBONATE ION × 2 P6G HEXAETHYLENE GLYCOL × 1 AE3 2-(2-ETHOXYETHOXY)ETHANOL × 2 HI6 4-(AMINOCARBONYL)-1-[({2-[(E)-(HYDROXYIMINO)METHYL]PYRIDINIUM-1-YL}METHOXY)METHYL]PYRIDINIUM × 2 X-RAY DIFFRACTION X-ray crystallization conditions:pH 7;pH 7 Resolution 2.40 Å R-free 0.213

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.

97 other PDB entries and 115 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ACES_MOUSE
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–543; UniProt 32–574 Author chain B; PDBConstruct 1–543; UniProt 32–574

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 5fpp

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id5fpp
Deposition date deposition_date2015-12-02
Structure title titleStructure of a pre-reaction ternary complex between sarin- acetylcholinesterase and HI-6
Keywords keywordsHYDROLASE, SARIN, HI-6, QM, DENSITY FUNCTIONAL THEORY CALCULATIONS, MICHAELIS COMPLEX.; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier37.81
Radius of gyration Rg (electron density) rg_electron37.69
Forward intensity I(0) i0211149000.00
Molecular weight molecular_weight119720.0 kDa
Excluded volume excluded_volume150340 ų
Envelope volume envelope_volume182610 ų
Hydration-shell volume shell_volume42128 ų
Envelope diameter envelope_diameter143.8
Shell Rg shell_rg41.53
Envelope Rg envelope_rg37.68
Shape Rg shape_rg37.66
Total Rg total_rg38.04
Total atoms total_atoms8467
Residues n_residues1072
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 dmax132.9
Rg (real space) rg_real38.20
Rg uncertainty (real space) rg_real_error1.33
I(0) (real space) i0_real2.1110e+08
I(0) uncertainty (real space) i0_real_error3.6980e+06
Rg (reciprocal space) rg_reciprocal37.97
I(0) (reciprocal space) i0_reciprocal211100000.0000
Solution quality estimate total_estimate0.7957
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary34.8
Skewness Skewness skewness0.513
Kurtosis Kurtosis kurtosis-0.488
Angular range angular_range— – 0.2100 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha60420000.0000
Real-space data points n_real_points43
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.558; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.783; Smooth: 0.883

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd5fppa1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.69 — alpha/beta-Hydrolases
Superfamily Superfamily superfamilyc.69.1 — alpha/beta-Hydrolases
Family Family familyc.69.1.1 — Acetylcholinesterase-like
Domain ID domain_idd5fppa2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd5fppb1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.69 — alpha/beta-Hydrolases
Superfamily Superfamily superfamilyc.69.1 — alpha/beta-Hydrolases
Family Family familyc.69.1.1 — Acetylcholinesterase-like
Domain ID domain_idd5fppb2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id5fppA00
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_id5fppB00
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)