6ESJ

Human butyrylcholinesterase in complex with propidium

PDB DOI: https://doi.org/10.2210/pdb6ESJ/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Drosophila melanogaster
Mutation(s): No

Deposited: 2017-10-20 Released: 2017-12-13
Deposition Author(s): Nachon, F., Brazzolotto, X., Wandhammer, M., Trovaslet-Leroy, M., Macdonald, I.R., Darvesh, S., Rosenberry, T.L.
Funding Organization(s): French Ministry of Armed Forces

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.98 Å
R-Value Free: 0.299
R-Value Work: 0.221
R-Value Observed: 0.224

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 123.83 kDa
Atom Count: 8,810
Modelled Residue Count: 1,053
Deposited Residue Count: 1,058
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cholinesterase	A, B	529	Homo sapiens	Mutation(s): 0 Gene Names: BCHE, CHE1 EC: 3.1.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for P06276 (Homo sapiens) Explore P06276 Go to UniProtKB: P06276
PHAROS: P06276 GTEx: ENSG00000114200
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P06276
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D, E, F	2		N-Glycosylation	Interactions Focus chain C Focus chain D Focus chain E Focus chain F Interactions & Density Focus chain C Focus chain D Focus chain E Focus chain F
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PRM (Subject of Investigation/LOI) Query on PRM Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain U [auth B] MOL2 format, chain J [auth A] MOL2 format, chain U [auth B]	J [auth A], U [auth B]	3,8-DIAMINO-5[3-(DIETHYLMETHYLAMMONIO)PROPYL]-6-PHENYLPHENANTHRIDINIUM C₂₇ H₃₄ N₄ ZDWVWKDAWBGPDN-UHFFFAOYSA-O		Interactions Focus chain J [auth A] Focus chain U [auth B] Interactions & Density Focus chain J [auth A] Focus chain U [auth B]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain N [auth B] SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain O [auth B] MOL2 format, chain H [auth A] MOL2 format, chain N [auth B] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain O [auth B]	G [auth A] H [auth A] I [auth A] K [auth B] L [auth B] G [auth A], H [auth A], I [auth A], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B]
GLY Query on GLY Download Ideal Coordinates CCD File SDF format, chain T [auth B] MOL2 format, chain T [auth B]	T [auth B]	GLYCINE C₂ H₅ N O₂ DHMQDGOQFOQNFH-UHFFFAOYSA-N		Interactions Focus chain T [auth B] Interactions & Density Focus chain T [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain S [auth B] SDF format, chain R [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B]	P [auth B], Q [auth B], R [auth B], S [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Interactions & Density Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.98 Å
R-Value Free: 0.299
R-Value Work: 0.221
R-Value Observed: 0.224
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.04	α = 90
b = 79.22	β = 90
c = 228.35	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
Coot	model building

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2017-12-13

Deposition Author(s):

Funding Organization	Location	Grant Number
French Ministry of Armed Forces	France	--

Revision History (Full details and data files)

Version 1.0: 2017-12-13
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2024-01-17
Changes: Data collection, Database references, Refinement description, Structure summary

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Help and Resources

6ESJ

Human butyrylcholinesterase in complex with propidium

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Entity ID: 2

Glycosylation Resources

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)