3D0Y: Protein S100-B

Crystal Structure of S100B in the Calcium and Zinc Loaded State at pH 6.5. Determined by X-ray diffraction at 1.5 Å resolution. Released 14 Apr 2009.

Method: X-ray diffraction
Resolution: 1.5 Å
Organism: Homo sapiens
Chains: 2
Atoms: 1,681
Mol. weight: 21.97 kDa
Ligands: ZN, CA
Released: 14 Apr 2009

Explore 3D0Y in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3D0Y contains 10 α-helices and 4 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	2-18	17
β-strand	27	1	1
α-helix	29-39	11
α-helix	45-47	3
α-helix	50-60	11
β-strand	68	1	1
α-helix	70-87	18

Chain B: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	2-18	17
β-strand	27	1	2
α-helix	29-39	11
α-helix	45-47	3
α-helix	50-60	11
β-strand	68	1	2
α-helix	70-88	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein S100-B	A	protein	92	Homo sapiens	P04271 (AlphaFold model)
Protein S100-B	B	protein	92	Homo sapiens	P04271 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3D0Y_1 Protein S100-B (chains A)
MSELEKAMVALIDVFHQYSGREGDKHKLKKSELKELINNELSHFLEEIKEQEVVDKVMET
LDNDGDGECDFQEFMAFVAMVTTACHEFFEHE

Sequence of entity 2 (B), FASTA

>3D0Y_2 Protein S100-B (chains B)
MSELEKAMVALIDVFHQYSGREGDKHKLKKSELKELINNELSHFLEEIKEQEVVDKVMET
LDNDGDGECDFQEFMAFVAMVTTACHEFFEHE

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
CA	Calcium ion	Ca	4

Water and common crystallization additives (PG4) are not listed.

Primary citation

The crystal structures of human S100B in the zinc- and calcium-loaded state at three pH values reveal zinc ligand swapping. Ostendorp, T., Diez, J., Heizmann, C.W. et al. Biochim Biophys Acta (2011) 1813:1083-1091. DOI 10.1016/j.bbamcr.2010.10.006 · PubMed

Other PDB entries of the same protein (UniProt P04271 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5D7F 1.3 Å, X-ray structure of Ca(2+)-S100B with human RAGE-derived W72 peptide
3CZT 1.4 Å, Crystal Structure of S100B in the Calcium and Zinc Loaded State at pH 9
3D10 1.65 Å, Crystal Structure of S100B in the Calcium and Zinc Loaded State at pH 10.0
2H61 1.9 Å, X-ray structure of human Ca2+-loaded S100B
3HCM 2.0 Å, Crystal structure of human S100B in complex with S45
5CSI 2.13 Å, S100B-RSK1 crystal structure A'
5CSF 2.4 Å, S100B-RSK1 crystal structure A
4XYN 2.55 Å, X-ray structure of Ca(2+)-S100B with human RAGE-derived W61 peptide
5CSJ 2.7 Å, S100B-RSK1 crystal structure B
5CSN 2.95 Å, S100B-RSK1 crystal structure C
1MQ1 Ca2+-S100B-TRTK-12 complex
1UWO Calcium form of human S100B, NMR, 20 structures

Browse structure collections

About this viewer

MolViewer shows 3D0Y directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.