3RD0 | pdb_00003rd0

Horse spleen apo-ferritin with bound thiopental

• PDB DOI: https://doi.org/10.2210/pdb3RD0/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Equus caballus
• Mutation(s): No 


• Deposited: 2011-03-31 Released: 2011-05-11 
• Deposition Author(s): Oakley, S.H., Vedula, L.S., Xi, J., Liu, R., Eckenhoff, R.G., Loll, P.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.205 (Depositor), 0.227 (DCC) 
• R-Value Work: 
  0.184 (Depositor) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Model: experimental

Literature

High resolution view of barbiturate recognition by a protein binding site

Oakley, S.H., Vedula, L.S., Xi, J., Liu, R., Eckenhoff, R.G., Loll, P.J.

To be published.

Biological Assembly 1  

Global Symmetry: Octahedral - O  (Explore in 3D)
Global Stoichiometry: Homo 24-mer - A24 

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

Macromolecule Content 

• Total Structure Weight: 20.87 kDa 
• Atom Count: 1,599 
• Modeled Residue Count: 168 
• Deposited Residue Count: 174 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferritin light chain	A	174	Equus caballus	Mutation(s): 0
UniProt
Find proteins for P02791 (Equus caballus) Explore P02791  Go to UniProtKB:  P02791

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDP	B [auth A]	5-ethyl-5-[(2R)-pentan-2-yl]-2-thioxodihydropyrimidine-4,6(1H,5H)-dione C11 H18 N2 O2 S IUJDSEJGGMCXSG-SSDOTTSWSA-N
CD	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N
SO4	H [auth A], I [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.205 (Depositor), 0.227 (DCC) 
• R-Value Work:  0.184 (Depositor) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: F 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 182.175	α = 90
b = 182.175	β = 90
c = 182.175	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
CrystalClear	data reduction
CrystalClear	data scaling
PHASER	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-05-11 
Deposition Author(s): Oakley, S.H., Vedula, L.S., Xi, J., Liu, R., Eckenhoff, R.G., Loll, P.J.

Revision History  

• Version 1.0: 2011-05-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2019-07-17
  Changes: Advisory, Data collection, Derived calculations, Refinement description
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description