2HRQ

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

PDB DOI: https://doi.org/10.2210/pdb2HRQ/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2006-07-20 Released: 2007-05-01
Deposition Author(s): Fleming, C.D., Redinbo, M.R.

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

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: 359.41 kDa
Atom Count: 26,340
Modelled Residue Count: 3,188
Deposited Residue Count: 3,192
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Liver carboxylesterase 1	A, B, C, D, E A, B, C, D, E, F	532	Homo sapiens	Mutation(s): 0 Gene Names: CES1 EC: 3.1.1.1
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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P23141
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose	G, H, I, J, K G, H, I, J, K, L	2		N/A	Interactions Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L Interactions & Density Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L
Glycosylation Resources
GlyTouCan: G05551OP GlyCosmos: G05551OP

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SIA Query on SIA Download Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain IA [auth E] SDF format, chain NA [auth F] SDF format, chain O [auth A] SDF format, chain T [auth B] SDF format, chain Z [auth C] MOL2 format, chain DA [auth D] MOL2 format, chain IA [auth E] MOL2 format, chain NA [auth F] MOL2 format, chain O [auth A] MOL2 format, chain T [auth B] MOL2 format, chain Z [auth C]	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		Interactions Focus chain DA [auth D] Focus chain IA [auth E] Focus chain NA [auth F] Focus chain O [auth A] Focus chain T [auth B] Focus chain Z [auth C] Interactions & Density Focus chain DA [auth D] Focus chain IA [auth E] Focus chain NA [auth F] Focus chain O [auth A] Focus chain T [auth B] Focus chain Z [auth C]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain HA [auth E] SDF format, chain MA [auth F] SDF format, chain N [auth A] SDF format, chain S [auth B] SDF format, chain Y [auth C] MOL2 format, chain CA [auth D] MOL2 format, chain HA [auth E] MOL2 format, chain MA [auth F] MOL2 format, chain N [auth A] MOL2 format, chain S [auth B] MOL2 format, chain Y [auth C]	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		Interactions Focus chain CA [auth D] Focus chain HA [auth E] Focus chain MA [auth F] Focus chain N [auth A] Focus chain S [auth B] Focus chain Y [auth C] Interactions & Density Focus chain CA [auth D] Focus chain HA [auth E] Focus chain MA [auth F] Focus chain N [auth A] Focus chain S [auth B] Focus chain Y [auth C]
GD7 Query on GD7 Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain GA [auth E] SDF format, chain KA [auth F] SDF format, chain M [auth A] SDF format, chain R [auth B] SDF format, chain W [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain GA [auth E] MOL2 format, chain KA [auth F] MOL2 format, chain M [auth A] MOL2 format, chain R [auth B] MOL2 format, chain W [auth C]	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		Interactions Focus chain BA [auth D] Focus chain GA [auth E] Focus chain KA [auth F] Focus chain M [auth A] Focus chain R [auth B] Focus chain W [auth C] Interactions & Density Focus chain BA [auth D] Focus chain GA [auth E] Focus chain KA [auth F] Focus chain M [auth A] Focus chain R [auth B] Focus chain W [auth C]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain EA [auth D] SDF format, chain FA [auth D] SDF format, chain JA [auth E] SDF format, chain LA [auth F] SDF format, chain OA [auth F] SDF format, chain P [auth A] SDF format, chain PA [auth F] SDF format, chain Q [auth A] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain X [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain EA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain JA [auth E] MOL2 format, chain LA [auth F] MOL2 format, chain OA [auth F] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth F] MOL2 format, chain Q [auth A] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain X [auth C]	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		Interactions Focus chain AA [auth C] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain JA [auth E] Focus chain LA [auth F] Focus chain OA [auth F] Focus chain P [auth A] Focus chain PA [auth F] Focus chain Q [auth A] Focus chain U [auth B] Focus chain V [auth B] Focus chain X [auth C] Interactions & Density Focus chain AA [auth C] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain JA [auth E] Focus chain LA [auth F] Focus chain OA [auth F] Focus chain P [auth A] Focus chain PA [auth F] Focus chain Q [auth A] Focus chain U [auth B] Focus chain V [auth B] Focus chain X [auth C]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900003 Query on PRD_900003	G, H, I, J, K G, H, I, J, K, L	sucrose	Oligosaccharide / Nutrient		Interactions Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L Interactions & Density Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Focus chain 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 = 55.463	α = 90
b = 181.193	β = 89.99
c = 203.051	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
AMoRE	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2007-05-01

Deposition Author(s):

Fleming, C.D.

Redinbo, M.R.

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