3D0Y

Crystal Structure of S100B in the Calcium and Zinc Loaded State at pH 6.5

Structural Biology Knowledgebase: 3D0Y SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.261
  • R-Value Work: 0.206

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3D0Y

Classification: METAL BINDING PROTEIN

Total Structure Weight: 21967.51

Macromolecule Entities
Molecule Chains Length Organism Details
Protein S100-B A 92 Homo sapiens Gene Name(s): S100B Gene View
Protein S100-B B 92 Homo sapiens Gene Name(s): S100B Gene View

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
PG4
Query on PG4

B TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A, B CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
FME
Query on FME
A L-PEPTIDE LINKING C6 H11 N O3 S MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.261
  • R-Value Work: 0.206
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 34.89 α = 90.00
b = 58.15 β = 111.12
c = 47.66 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-05-02
  • Released Date: 2009-04-14
  • Deposition author(s): Ostendorp, T., Diez, J., Heizmann, C.W., Fritz, G.

Revision History

  • 2011-07-13
    Type: Flag residual B-value | Details: Tagged residual B temperature factor
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4