7PSP | pdb_00007psp

Crystal structure of S100A4 labeled with NU000846b.

• PDB DOI: https://doi.org/10.2210/pdb7PSP/pdb

• Classification: CYTOSOLIC PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2021-09-23 Released: 2022-10-05 
• Deposition Author(s): Giroud, C., Szommer, T., Coxon, C., Monteiro, O., Christott, T., Bennett, J., Aitmakhanova, K., Raux, B., Newman, J., Elkins, J., Arruda Bezerra, G., Krojer, T., Koekemoer, L., Von Delft, F., Bountr, C., Brennan, P., Fedorov, O.
• Funding Organization(s): Innovative Medicines Initiative

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.61 Å
• R-Value Free: 
  0.286 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.245 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.247 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of S100A4 labeled with NU000846b.

Giroud, C.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 29.54 kDa 
• Atom Count: 1,555 
• Modeled Residue Count: 192 
• Deposited Residue Count: 246 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein S100-A4	A, B	123	Homo sapiens	Mutation(s): 0  Gene Names: S100A4, CAPL, MTS1
UniProt & NIH Common Fund Data Resources
Find proteins for P26447 (Homo sapiens) Explore P26447  Go to UniProtKB:  P26447
PHAROS:  P26447 GTEx:  ENSG00000196154

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
85Q (Subject of Investigation/LOI)	C [auth A], F [auth B]	(2R,4R)-1-(2-chloranylethanoyl)-N-(3-chlorophenyl)-4-phenyl-pyrrolidine-2-carboxamide C19 H18 Cl2 N2 O2 WELUOUAMWVTFIH-WMLDXEAASA-N
CA	D [auth A], E [auth A], G [auth B], H [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.61 Å
• R-Value Free:  0.286 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.245 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.247 (Depositor) 

Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.54	α = 90
b = 109.54	β = 90
c = 89.87	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-10-05 
Deposition Author(s): Giroud, C., Szommer, T., Coxon, C., Monteiro, O., Christott, T., Bennett, J., Aitmakhanova, K., Raux, B., Newman, J., Elkins, J., Arruda Bezerra, G., Krojer, T., Koekemoer, L., Von Delft, F., Bountr, C., Brennan, P., Fedorov, O.

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Funding Organization	Location	Grant Number
Innovative Medicines Initiative	Switzerland	115766

Revision History  

• Version 1.0: 2022-10-05
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary