2HRQ

Crystal structure of Human Liver Carboxylesterase 1 (hCE1) in covalent complex with the nerve agent Soman (GD)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.170 

Starting Model: experimental
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This is version 3.0 of the entry. See complete history


Literature

Crystal Structures of Human Carboxylesterase 1 in Covalent Complexes with the Chemical Warfare Agents Soman and Tabun.

Fleming, C.D.Edwards, C.C.Kirby, S.D.Maxwell, D.M.Potter, P.M.Cerasoli, D.M.Redinbo, M.R.

(2007) Biochemistry 46: 5063-5071

  • DOI: https://doi.org/10.1021/bi700246n
  • Primary Citation of Related Structures:  
    2HRQ, 2HRR

  • PubMed Abstract: 

    The organophosphorus nerve agents sarin, soman, tabun, and VX exert their toxic effects by inhibiting the action of human acetylcholinesterase, a member of the serine hydrolase superfamily of enzymes. The current treatments for nerve agent exposure must be administered quickly to be effective, and they often do not eliminate long-term toxic side effects associated with organophosphate poisoning. Thus, there is significant need for effective prophylactic methods to protect at-risk personnel from nerve agent exposure, and protein-based approaches have emerged as promising candidates. We present the 2.7 A resolution crystal structures of the serine hydrolase human carboxylesterase 1 (hCE1), a broad-spectrum drug metabolism enzyme, in covalent acyl-enzyme intermediate complexes with the chemical weapons soman and tabun. The structures reveal that hCE1 binds stereoselectively to these nerve agents; for example, hCE1 appears to react preferentially with the 10(4)-fold more lethal PS stereoisomer of soman relative to the PR form. In addition, structural features of the hCE1 active site indicate that the enzyme may be resistant to dead-end organophosphate aging reactions that permanently inactivate other serine hydrolases. Taken together, these data provide important structural details toward the goal of engineering hCE1 into an organophosphate hydrolase and protein-based therapeutic for nerve agent exposure.


  • Organizational Affiliation

    Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Liver carboxylesterase 1
A, B, C, D, E
A, B, C, D, E, F
532Homo sapiensMutation(s): 0 
Gene Names: CES1
EC: 3.1.1.1 (PDB Primary Data), 3.1.1.56 (UniProt), 3.1.1.13 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P23141 (Homo sapiens)
Explore P23141 
Go to UniProtKB:  P23141
PHAROS:  P23141
GTEx:  ENSG00000198848 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23141
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P23141-1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose
G, H, I, J, K
G, H, I, J, K, L
2N/A
Glycosylation Resources
GlyTouCan:  G05551OP
GlyCosmos:  G05551OP
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SIA
Query on SIA

Download Ideal Coordinates CCD File 
DA [auth D]
IA [auth E]
NA [auth F]
O [auth A]
T [auth B]
DA [auth D],
IA [auth E],
NA [auth F],
O [auth A],
T [auth B],
Z [auth C]
N-acetyl-alpha-neuraminic acid
C11 H19 N O9
SQVRNKJHWKZAKO-YRMXFSIDSA-N
NAG
Query on NAG

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CA [auth D]
HA [auth E]
MA [auth F]
N [auth A]
S [auth B]
CA [auth D],
HA [auth E],
MA [auth F],
N [auth A],
S [auth B],
Y [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
GD7
Query on GD7

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BA [auth D]
GA [auth E]
KA [auth F]
M [auth A]
R [auth B]
BA [auth D],
GA [auth E],
KA [auth F],
M [auth A],
R [auth B],
W [auth C]
(1R)-1,2,2-TRIMETHYLPROPYL (R)-METHYLPHOSPHINATE
C7 H17 O2 P
QZUGWOMGKDLYKO-ZCFIWIBFSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth C]
EA [auth D]
FA [auth D]
JA [auth E]
LA [auth F]
AA [auth C],
EA [auth D],
FA [auth D],
JA [auth E],
LA [auth F],
OA [auth F],
P [auth A],
PA [auth F],
Q [auth A],
U [auth B],
V [auth B],
X [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.170 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.463α = 90
b = 181.193β = 89.99
c = 203.051γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-05-01
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2023-08-30
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 3.0: 2024-12-25
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary