1MX9 | pdb_00001mx9

Crystal Structure of Human Liver Carboxylesterase in complexed with naloxone methiodide, a heroin analogue


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 
    0.280 (Depositor) 
  • R-Value Work: 
    0.214 (Depositor) 
  • R-Value Observed: 
    0.214 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1MX9

This is version 1.4 of the entry. See complete history

Literature

Structural Basis of Heroin and Cocaine Metabolism by a Promiscuous Human Drug-Processing Enzyme

Bencharit, S.Morton, C.L.Xue, Y.Potter, P.M.Redinbo, M.R.

(2003) Nat Struct Biol 10: 349-356

  • DOI: https://doi.org/10.1038/nsb919
  • Primary Citation Related Structures: 
    1MX5, 1MX9

  • PubMed Abstract: 

    We present the first crystal structures of a human protein bound to analogs of cocaine and heroin. Human carboxylesterase 1 (hCE1) is a broad-spectrum bioscavenger that catalyzes the hydrolysis of heroin and cocaine, and the detoxification of organophosphate chemical weapons, such as sarin, soman and tabun. Crystal structures of the hCE1 glycoprotein in complex with the cocaine analog homatropine and the heroin analog naloxone provide explicit details about narcotic metabolism in humans. The hCE1 active site contains both specific and promiscuous compartments, which enable the enzyme to act on structurally distinct chemicals. A selective surface ligand-binding site regulates the trimer-hexamer equilibrium of hCE1 and allows each hCE1 monomer to bind two narcotic molecules simultaneously. The bioscavenger properties of hCE1 can likely be used to treat both narcotic overdose and chemical weapon exposure.


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

Macromolecule Content 

  • Total Structure Weight: 733.12 kDa 
  • Atom Count: 51,134 
  • Modeled Residue Count: 6,378 
  • Deposited Residue Count: 6,576 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
liver Carboxylesterase I
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
548Homo sapiensMutation(s): 0 
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
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NLX

Query on NLX



Download:Ideal Coordinates CCD File
AA [auth G]
CA [auth H]
EA [auth I]
GA [auth J]
IA [auth K]
AA [auth G],
CA [auth H],
EA [auth I],
GA [auth J],
IA [auth K],
KA [auth L],
O [auth A],
Q [auth B],
S [auth C],
U [auth D],
W [auth E],
Y [auth F]
(5A,17R)-4,5-EPOXY-3,14-DIHYDROXY-17-METHYL-6-OXO-17-(2-PROPENYL)-MORPHINANIUM
C20 H24 N O4
PCSQOABIHJXZMR-YNUHATHGSA-O
NAG

Query on NAG



Download:Ideal Coordinates CCD File
BA [auth H]
DA [auth I]
FA [auth J]
HA [auth K]
JA [auth L]
BA [auth H],
DA [auth I],
FA [auth J],
HA [auth K],
JA [auth L],
M [auth A],
N [auth A],
P [auth B],
R [auth C],
T [auth D],
V [auth E],
X [auth F],
Z [auth G]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free:  0.280 (Depositor) 
  • R-Value Work:  0.214 (Depositor) 
  • R-Value Observed: 0.214 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.174α = 90.28
b = 120.711β = 89.32
c = 177.017γ = 99.22
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-04-08
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary
  • Version 1.4: 2024-10-16
    Changes: Data collection, Database references, Structure summary