2XMD

G117H mutant of human butyrylcholinesterase in complex with echothiophate

PDB DOI: https://doi.org/10.2210/pdb2XMD/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Cricetulus griseus
Mutation(s): Yes

Deposited: 2010-07-27 Released: 2010-12-01
Deposition Author(s): Nachon, F., Carletti, E., Wandhammer, M., Nicolet, Y., Schopfer, L.M., Masson, P., Lockridge, O.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.214
R-Value Work: 0.170
R-Value Observed: 0.172

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: 62.71 kDa
Atom Count: 4,705
Modelled Residue Count: 527
Deposited Residue Count: 529
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CHOLINESTERASE	A	529	Homo sapiens	Mutation(s): 5 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

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	B, C	3		N-Glycosylation	Interactions Focus chain B Focus chain C Interactions & Density Focus chain B Focus chain C
Glycosylation Resources
GlyTouCan: G28454KX GlyCosmos: G28454KX GlyGen: G28454KX

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	D	3		N-Glycosylation	Interactions Focus chain D Interactions & Density Focus chain D
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain HA [auth A] SDF format, chain IA [auth A] SDF format, chain JA [auth A] MOL2 format, chain HA [auth A] MOL2 format, chain IA [auth A] MOL2 format, chain JA [auth A]	HA [auth A], IA [auth A], JA [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain HA [auth A] Focus chain IA [auth A] Focus chain JA [auth A] Interactions & Density Focus chain HA [auth A] Focus chain IA [auth A] Focus chain JA [auth A]
DEP Query on DEP Download Ideal Coordinates CCD File SDF format, chain Z [auth A] MOL2 format, chain Z [auth A]	Z [auth A]	DIETHYL PHOSPHONATE C₄ H₁₁ O₃ P MJUJXFBTEFXVKU-UHFFFAOYSA-N		Interactions Focus chain Z [auth A] Interactions & Density Focus chain Z [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain AA [auth A] MOL2 format, chain AA [auth A]	AA [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth A] Interactions & Density Focus chain AA [auth A]
BR Query on BR Download Ideal Coordinates CCD File SDF format, chain EA [auth A] MOL2 format, chain EA [auth A]	EA [auth A]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M		Interactions Focus chain EA [auth A] Interactions & Density Focus chain EA [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain GA [auth A] MOL2 format, chain GA [auth A]	GA [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain GA [auth A] Interactions & Density Focus chain GA [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain BA [auth A] SDF format, chain CA [auth A] SDF format, chain DA [auth A] SDF format, chain KA [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain CA [auth A] MOL2 format, chain DA [auth A] MOL2 format, chain KA [auth A]	BA [auth A], CA [auth A], DA [auth A], KA [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain BA [auth A] Focus chain CA [auth A] Focus chain DA [auth A] Focus chain KA [auth A] Interactions & Density Focus chain BA [auth A] Focus chain CA [auth A] Focus chain DA [auth A] Focus chain KA [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain FA [auth A] SDF format, chain LA [auth A] MOL2 format, chain FA [auth A] MOL2 format, chain LA [auth A]	FA [auth A], LA [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain FA [auth A] Focus chain LA [auth A] Interactions & Density Focus chain FA [auth A] Focus chain LA [auth A]
UNX Query on UNX Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain K [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain R [auth A] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain W [auth A] SDF format, chain X [auth A] SDF format, chain Y [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain S [auth A] MOL2 format, chain H [auth A] MOL2 format, chain K [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain R [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A] MOL2 format, chain X [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain S [auth A]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A], X [auth A], Y [auth A]	UNKNOWN ATOM OR ION X		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.214
R-Value Work: 0.170
R-Value Observed: 0.172
Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 154.88	α = 90
b = 154.88	β = 90
c = 127.53	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-12-01

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-12-01
Type: Initial release
Version 1.1: 2011-11-16
Changes: Database references, Refinement description, Version format compliance
Version 1.2: 2019-01-30
Changes: Data collection, Experimental preparation, Other
Version 1.3: 2019-02-06
Changes: Data collection, Experimental preparation
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary
Version 2.1: 2023-12-20
Changes: Data collection, Database references, Refinement description, Structure summary