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 
- Funding Organization(s): National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)
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 
This is version 2.1 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Phosphatidylcholine-sterol acyltransferase | 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  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P04180 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
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 |
Small Molecules
Ligands 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on 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 Name | Purpose |
---|---|
REFMAC | refinement |
XDS | data scaling |
Aimless | data scaling |
PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2017-10-25  Deposition Author(s): Manthei, K.A., Glukhova, A., Tesmer, J.J.G.
Funding Organization | Location | Grant Number |
---|---|---|
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI) | United States | HL122416 |
Revision History (Full details and data files)
- 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