5D7F

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.158 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

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

Jensen, J.L.Colbert, C.L.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein S100-B
A, B
92Homo sapiensMutation(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 Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04271
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Advanced glycosylation end product-specific receptorC [auth P]15Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q15109 (Homo sapiens)
Explore Q15109 
Go to UniProtKB:  Q15109
PHAROS:  Q15109
GTEx:  ENSG00000204305 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15109
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
I [auth A]
J [auth A]
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
Query on CA

Download Ideal Coordinates CCD File 
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 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.158 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.089α = 90
b = 59.824β = 111.65
c = 47.563γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
PHASERphasing
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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