5D7F | pdb_00005d7f

X-ray structure of Ca(2+)-S100B with human RAGE-derived W72 peptide

• PDB DOI: https://doi.org/10.2210/pdb5D7F/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-08-13 Released: 2016-08-17 
• Deposition Author(s): Jensen, J.L., Colbert, C.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 
  0.183 (Depositor), 0.185 (DCC) 
• R-Value Work: 
  0.157 (Depositor), 0.159 (DCC) 
• R-Value Observed: 
  0.158 (Depositor) 

Starting Model: experimental

Literature

X-ray structure of Ca(2+)-S100B with human RAGE-derived W72 peptide

Jensen, J.L., Colbert, C.L.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

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

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

Macromolecule Content 

• Total Structure Weight: 23.69 kDa 
• Atom Count: 2,017 
• Modeled Residue Count: 192 
• Deposited Residue Count: 199 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein S100-B	A, B	92	Homo sapiens	Mutation(s): 0  Gene Names: S100B
UniProt & NIH Common Fund Data Resources
Find proteins for P04271 (Homo sapiens) Explore P04271  Go to UniProtKB:  P04271
PHAROS:  P04271 GTEx:  ENSG00000160307

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Advanced glycosylation end product-specific receptor	C [auth P]	15	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q15109 (Homo sapiens) Explore Q15109  Go to UniProtKB:  Q15109
PHAROS:  Q15109 GTEx:  ENSG00000204305

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], M [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	D [auth A], E [auth A], K [auth B], L [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free:  0.183 (Depositor), 0.185 (DCC) 
• R-Value Work:  0.157 (Depositor), 0.159 (DCC) 
• R-Value Observed: 0.158 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.089	α = 90
b = 59.824	β = 111.65
c = 47.563	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
PHASER	phasing
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-08-17 
Deposition Author(s): Jensen, J.L., Colbert, C.L.

Revision History  

• Version 1.0: 2016-08-17
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description