3V1W | pdb_00003v1w

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 (Depositor), 0.221 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.174 (Depositor) 

Starting Model: experimental

Literature

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

Subramanian, A.K., Nissen, M.N., Lewis, K.M., Sanchez, E.J., Muralidharan, A.K., Kang, C.

To be published.

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 
• Modeled 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
Glycosylation
Glycosylation Sites: 1

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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 (Depositor), 0.221 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.174 (Depositor) 

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
• Version 2.2: 2024-11-06
  Changes: Structure summary