5D7F: Ca(2+)-S100B with human RAGE-derived W72 peptide

X-ray structure of Ca(2+)-S100B with human RAGE-derived W72 peptide. Determined by X-ray diffraction at 1.3 Å resolution. Released 17 Aug 2016.

Method: X-ray diffraction
Resolution: 1.3 Å
Organism: Homo sapiens
Chains: 3
Atoms: 2,017
Mol. weight: 23.69 kDa
Ligands: CA
Released: 17 Aug 2016

Explore 5D7F in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5D7F contains 10 α-helices and 6 β-strands across 3 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	3-19	17
β-strand	28	1	1
α-helix	30-40	11
α-helix	46-48	3
α-helix	51-61	11
β-strand	69	1	1
α-helix	71-84	14

Chain B: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	3-19	17
β-strand	28	1	2
α-helix	30-40	11
β-strand	45	1	3
α-helix	46-48	3
α-helix	51-61	11
β-strand	69	1	2
α-helix	71-84	14

Chain P: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	5	1	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein S100-B	A, B	protein	92	Homo sapiens	P04271 (AlphaFold model)
Advanced glycosylation end product-specific receptor	P	protein	15	Homo sapiens	Q15109 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5D7F_1 Protein S100-B (chains A, B)
MSELEKAMVALIDVFHQYSGREGDKHKLKKSELKELINNELSHFLEEIKEQEVVDKVMET
LDNDGDGECDFQEFMAFVAMVTTACHEFFEHE

Sequence of entity 2 (P), FASTA

>5D7F_2 Advanced glycosylation end product-specific receptor (chains P)
SPQGGGPWDSVARVL

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	4

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

Primary citation

X-ray structure of Ca(2+)-S100B with human RAGE-derived W72 peptide. Jensen, J.L., Colbert, C.L. To be published.

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

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
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

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