3HCM: Human S100B

Crystal structure of human S100B in complex with S45. Determined by X-ray diffraction at 2.0 Å resolution. Released 2 Feb 2010.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 2
Atoms: 1,611
Mol. weight: 22.2 kDa
Ligands: S45, CA
Released: 2 Feb 2010

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

Secondary structure: helices and β-sheets

3HCM 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	70-85	16

Chain B: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	2-18	17
β-strand	26-27	2	2
α-helix	29-39	11
α-helix	45-47	3
α-helix	50-60	11
β-strand	68-69	2	2
α-helix	70-87	18

Molecules and chains

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

Sequence of entity 1 (A, B), FASTA

>3HCM_1 Protein S100-B (chains A, B)
MSELEKAMVALIDVFHQYSGREGDKHKLKKSELKELINNELSHFLEEIKEQEVVDKVMET
LDNDGDGECDFQEFMAFVAMVTTACHEFFEHE

Ligands and cofactors

ID	Name	Formula	Copies
S45	(3R)-3-[3-(4-chlorophenyl)-1,2,4-oxadiazol-5-yl]piperidine	C13 H14 Cl N3 O	2
CA	Calcium ion	Ca	4

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

Primary citation

Fragmenting the S100B-p53 Interaction: Combined Virtual/Biophysical Screening Approaches to Identify Ligands. Agamennone, M., Cesari, L., Lalli, D. et al. ChemMedChem (2010) 5:428-435. DOI 10.1002/cmdc.200900393 · 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
3D0Y 1.5 Å, Crystal Structure of S100B in the Calcium and Zinc Loaded State at pH 6.5
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
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

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