3V1W

Molecular Basis for Multiple Ligand Binding of Calsequestrin and Potential Inhibition by Caffeine and Gallocatecin

• PDB DOI: https://doi.org/10.2210/pdb3V1W/pdb

• Classification: CALCIUM BINDING PROTEIN
• Organism(s): Oryctolagus cuniculus
• Mutation(s): No 


• Deposited: 2011-12-10 Released: 2012-12-12 
• Deposition Author(s): Subramanian, A.K., Nissen, M.N., Lewis, K.M., Sanchez, E.J., Muralidharan, A.K., Kang, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free: 0.222 
• R-Value Work: 0.171 
• R-Value Observed: 0.174 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 43.45 kDa 
• Atom Count: 3,438 
• Modelled Residue Count: 349 
• Deposited Residue Count: 367 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calsequestrin-1	A	367	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for P07221 (Oryctolagus cuniculus) Explore P07221  Go to UniProtKB:  P07221

Oligosaccharides

Help

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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MRD	E [auth A]	(4R)-2-METHYLPENTANE-2,4-DIOL C6 H14 O2 SVTBMSDMJJWYQN-RXMQYKEDSA-N
MPD	C [auth A], D [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
CA	F [auth A], G [auth A], H [auth A], I [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA	J [auth A], K [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free: 0.222 
• R-Value Work: 0.171 
• R-Value Observed: 0.174 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.082	α = 90
b = 144.592	β = 90
c = 110.965	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-12-12 
Deposition Author(s): Subramanian, A.K., Nissen, M.N., Lewis, K.M., Sanchez, E.J., Muralidharan, A.K., Kang, C.

Revision History  

• Version 1.0: 2012-12-12
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-09-13
  Changes: Advisory, Data collection, Database references, Refinement description, Structure summary