5DEJ | pdb_00005dej

Transthyretin natural mutant A19D

• PDB DOI: https://doi.org/10.2210/pdb5DEJ/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2015-08-25 Released: 2016-08-31 
• Deposition Author(s): Pereira, H.M., Ferreira, P., Andrade, C., Lima, C., Palhano, F., Foguel, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.37 Å
• R-Value Free: 
  0.207 (Depositor), 0.208 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Literature

Crystal structure of human Transthyretin natural mutant A19D

Ferreira, P., Pereira, H.M., Andrade, C., Lima, C., Palhano, F., Foguel, D.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 25.53 kDa 
• Atom Count: 2,000 
• Modeled Residue Count: 231 
• Deposited Residue Count: 232 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transthyretin	A, B	116	Homo sapiens	Mutation(s): 1  Gene Names: TTR, PALB
UniProt & NIH Common Fund Data Resources
Find proteins for P02766 (Homo sapiens) Explore P02766  Go to UniProtKB:  P02766
PHAROS:  P02766 GTEx:  ENSG00000118271

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.37 Å
• R-Value Free:  0.207 (Depositor), 0.208 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.93	α = 90
b = 41.75	β = 90
c = 62.74	γ = 90

Software Package:

Software Name	Purpose
xia2	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-08-31 
Deposition Author(s): Pereira, H.M., Ferreira, P., Andrade, C., Lima, C., Palhano, F., Foguel, D.

Revision History  

• Version 1.0: 2016-08-31
  Type: Initial release
  
• Version 2.0: 2020-01-15
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2024-03-06
  Changes: Advisory, Data collection, Database references