Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 40.70 kDa 
• Atom Count: 2928 
• Modelled Residue Count: 346 
• Deposited Residue Count: 346 
• Unique protein chains: 1

1ALW

INHIBITOR AND CALCIUM BOUND DOMAIN VI OF PORCINE CALPAIN

• PDB DOI: 10.2210/pdb1ALW/pdb

• Classification: CALCIUM BINDING
• Organism(s): Sus scrofa
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1997-06-04 Released: 1998-06-10 
• Deposition Author(s): Narayana, S.V.L., Lin, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free: 0.270 
• R-Value Work: 0.210 
• R-Value Observed: 0.210 

Literature

Crystal structure of calcium bound domain VI of calpain at 1.9 A resolution and its role in enzyme assembly, regulation, and inhibitor binding.

Lin, G.D., Chattopadhyay, D., Maki, M., Wang, K.K., Carson, M., Jin, L., Yuen, P.W., Takano, E., Hatanaka, M., DeLucas, L.J., Narayana, S.V.

(1997) Nat Struct Biol 4: 539-547

• PubMed: 9228946 
• DOI: 10.1038/nsb0797-539
• Primary Citation of Related Structures:  
  1ALV, 1ALW


• PubMed Abstract: 
  

The three dimensional structure of calcium-bound domain VI of porcine calpain has been determined to 1.9 A resolution. The crystal structure reveals five EF-hands, one more than previously suggested. There are two EF-hand pairs, one pair (EF1-EF2) displays an 'open' conformation and the other (EF3-EF4) a 'closed' conformation. Unusually, a calcium atom is found at the C-terminal end of the calcium binding loop of EF4. With two additional residues in the calcium binding loop, the fifth EF-hand (EF5) is in a 'closed' conformation. EF5 pairs up with the corresponding fifth EF-hand of a non-crystallographically related molecule. Considering the EF5's role in a homodimer formation of domain VI, we suggest a model for the assembly of heterodimeric calpain. The crystal structure of a Ca2+ bound domain VI-inhibitor (PD150606) complex has been refined to 2.1 A resolution. A possible mode for calpain inhibition is discussed.

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Organizational Affiliation: 

Center for Macromolecular Crystallography, University of Alabama at Birmingham 35294, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CALPAIN	A, B	173	Sus scrofa	Mutation(s): 0  Gene Names: CAPNS1, CAPN4
UniProt
Find proteins for P04574 (Sus scrofa) Explore P04574  Go to UniProtKB:  P04574

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ISA	G [auth A], L [auth B]	3-(4-IODO-PHENYL)-2-MERCAPTO-PROPIONIC ACID C9 H9 I O2 S MXQYDIIKDPMYMF-QMMMGPOBSA-N
CA	C [auth A], D [auth A], E [auth A], F [auth A], H [auth B], I [auth B], J [auth B], K [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
ISA	PDBBind:  1ALW	Ki: 300 (nM) from 1 assay(s)
	Binding MOAD:  1ALW	Ki: 300 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free: 0.270 
• R-Value Work: 0.210 
• R-Value Observed: 0.210 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.87	α = 90
b = 80.46	β = 91.2
c = 57.08	γ = 90

Software Package:

Software Name	Purpose
PHASES	phasing
X-PLOR	refinement
XGEN	data reduction
XGEN	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1997-06-04 
• Released Date: 1998-06-10 
Deposition Author(s): Narayana, S.V.L., Lin, G.

Revision History  

• Version 1.0: 1998-06-10
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2012-05-02
  Changes: Structure summary