4DIR

2.6 Angstrom X-ray structure of human CA(2+)-S100A5

• PDB DOI: https://doi.org/10.2210/pdb4DIR/pdb

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


• Deposited: 2012-01-31 Released: 2013-02-13 
• Deposition Author(s): Liriano, M.A., Toth, E.A., Weber, D.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.283 
• R-Value Work: 0.243 
• R-Value Observed: 0.245 

Literature

Target-binding to S100A5 changes Ca(2+)-binding affinity and dynamics.

Liriano, M.A., Varney, K.M., Ishima, R., Toth, E.A., Weber, D.J.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 21.68 kDa 
• Atom Count: 1,201 
• Modelled Residue Count: 161 
• Deposited Residue Count: 184 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein S100-A5	A, B	92	Homo sapiens	Mutation(s): 0  Gene Names: S100A5, S100D
UniProt & NIH Common Fund Data Resources
Find proteins for P33763 (Homo sapiens) Explore P33763  Go to UniProtKB:  P33763
PHAROS:  P33763 GTEx:  ENSG00000196420

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.283 
• R-Value Work: 0.243 
• R-Value Observed: 0.245 
• Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.692	α = 90
b = 52.692	β = 90
c = 67.012	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASES	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-02-13 
Deposition Author(s): Liriano, M.A., Toth, E.A., Weber, D.J.

Revision History  

• Version 1.0: 2013-02-13
  Type: Initial release
  
• Version 1.1: 2024-02-28
  Changes: Data collection, Database references, Derived calculations