5TXF

Crystal structure of Lecithin:cholesterol acyltransferase (LCAT) in a closed conformation

• PDB DOI: https://doi.org/10.2210/pdb5TXF/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2016-11-16 Released: 2017-10-25 
• Deposition Author(s): Manthei, K.A., Glukhova, A., Tesmer, J.J.G.
• Funding Organization(s): National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.267 
• R-Value Work: 0.250 
• R-Value Observed: 0.250 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 195.47 kDa 
• Atom Count: 12,410 
• Modelled Residue Count: 1,512 
• Deposited Residue Count: 1,688 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylcholine-sterol acyltransferase	A, B, C, D	422	Homo sapiens	Mutation(s): 0  Gene Names: LCAT EC: 2.3.1.43 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P04180 (Homo sapiens) Explore P04180  Go to UniProtKB:  P04180
PHAROS:  P04180 GTEx:  ENSG00000213398

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, G, I, J	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	K [auth A], L [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.267 
• R-Value Work: 0.250 
• R-Value Observed: 0.250 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.887	α = 90
b = 123.532	β = 96.19
c = 114.778	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data scaling
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-10-25 
Deposition Author(s): Manthei, K.A., Glukhova, A., Tesmer, J.J.G.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	HL122416

Revision History  

• Version 1.0: 2017-10-25
  Type: Initial release
  
• Version 1.1: 2017-11-01
  Changes: Database references
• Version 1.2: 2017-12-20
  Changes: Database references
• Version 1.3: 2019-12-04
  Changes: Author supporting evidence
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-10-04
  Changes: Data collection, Database references, Refinement description, Structure summary