1YR5 | pdb_00001yr5

1.7-A structure of calmodulin bound to a peptide from DAP kinase

• PDB DOI: https://doi.org/10.2210/pdb1YR5/pdb

• Classification: METAL BINDING PROTEIN/TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-02-03 Released: 2006-07-04 
• Deposition Author(s): Kursula, P., Vahokoski, J., Wilmanns, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.257 (Depositor), 0.262 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.215 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: experimental

Literature

Recognition of human death-associated protein kinases by calmodulin

Kursula, P., Vahokoski, J., Wilmanns, M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 19.27 kDa 
• Atom Count: 1,595 
• Modeled Residue Count: 165 
• Deposited Residue Count: 167 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
calmodulin	A	148	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P0DP23 (Homo sapiens) Explore P0DP23  Go to UniProtKB:  P0DP23
PHAROS:  P0DP23 GTEx:  ENSG00000198668

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
19-mer from Death-associated protein kinase 1	B	19	N/A	Mutation(s): 0  EC: 2.7.1.37 (PDB Primary Data), 2.7.11.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P53355 (Homo sapiens) Explore P53355  Go to UniProtKB:  P53355
PHAROS:  P53355 GTEx:  ENSG00000196730

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.257 (Depositor), 0.262 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.215 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.07	α = 90
b = 33.71	β = 111.16
c = 75.89	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-07-04 
Deposition Author(s): Kursula, P., Vahokoski, J., Wilmanns, M.

Revision History  

• Version 1.0: 2006-07-04
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2019-11-20
  Changes: Data collection, Derived calculations
• Version 1.4: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description