2VJB

Torpedo Californica Acetylcholinesterase In Complex With A Non Hydrolysable Substrate Analogue, 4-Oxo-N,N,N- Trimethylpentanaminium - Orthorhombic space group - Dataset D at 100K

PDB DOI: https://doi.org/10.2210/pdb2VJB/pdb

Classification: HYDROLASE
Organism(s): Tetronarce californica
Mutation(s): No

Deposited: 2007-12-09 Released: 2008-07-22
Deposition Author(s): Colletier, J.P., Bourgeois, D., Fournier, D., Silman, I., Sussman, J.L., Weik, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.39 Å
R-Value Free: 0.244
R-Value Work: 0.190
R-Value Observed: 0.190

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.6 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 123.54 kDa
Atom Count: 10,185
Modelled Residue Count: 1,060
Deposited Residue Count: 1,074
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ACETYLCHOLINESTERASE	A, B	537	Tetronarce californica	Mutation(s): 0 EC: 3.1.1.7
UniProt
Find proteins for P04058 (Tetronarce californica) Explore P04058 Go to UniProtKB: P04058
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P04058
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B]	C [auth A], D [auth A], L [auth B], M [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain L [auth B] Focus chain M [auth B]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain Q [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain Q [auth B]	H [auth A], I [auth A], Q [auth B]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain Q [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain Q [auth B]
CCD Query on CCD Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B]	F [auth A], G [auth A], O [auth B], P [auth B]	(4R)-4-HYDROXY-N,N,N-TRIMETHYLPENTAN-1-AMINIUM C₈ H₂₀ N O HSBSNRZAOXKTSK-MRVPVSSYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain O [auth B] Focus chain P [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain N [auth B] MOL2 format, chain E [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain N [auth B]	E [auth A], J [auth A], K [auth A], N [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B] Interactions & Density Focus chain E [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.39 Å
R-Value Free: 0.244
R-Value Work: 0.190
R-Value Observed: 0.190
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.07	α = 90
b = 107.29	β = 90
c = 151.49	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
XDS	data reduction
XSCALE	data scaling
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-07-22

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-07-22
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2019-04-03
Changes: Data collection, Derived calculations, Experimental preparation, Other
Version 1.4: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Data collection, Derived calculations, Other, Structure summary
Version 1.5: 2021-05-12
Changes: Derived calculations, Structure summary
Version 1.6: 2023-12-13
Changes: Data collection, Database references, Refinement description

Prepare Data

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Deposit Data

Help and Resources

2VJB

Torpedo Californica Acetylcholinesterase In Complex With A Non Hydrolysable Substrate Analogue, 4-Oxo-N,N,N- Trimethylpentanaminium - Orthorhombic space group - Dataset D at 100K

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)