4XYN: Ca(2+)-S100B with human RAGE-derived W61 peptide
X-ray structure of Ca(2+)-S100B with human RAGE-derived W61 peptide. Determined by X-ray diffraction at 2.55 Å resolution. Released 13 May 2015.
- Method
- X-ray diffraction
- Resolution
- 2.55 Å
- Organisms
- synthetic construct, Homo sapiens
- Chains
- 5
- Atoms
- 3,046
- Mol. weight
- 44.87 kDa
- Ligands
- CA
- Released
- 13 May 2015
Explore 4XYN in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
4XYN contains 22 α-helices and 10 β-strands across 5 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: 6 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 | 1 |
| α-helix | 46-48 | 3 | |
| α-helix | 51-61 | 11 | |
| β-strand | 69 | 1 | 2 |
| α-helix | 71-86 | 16 | |
| α-helix | 87-89 | 3 | |
Chain B: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-19 | 17 | |
| β-strand | 27-28 | 2 | 3 |
| α-helix | 30-40 | 11 | |
| α-helix | 46-48 | 3 | |
| α-helix | 51-61 | 11 | |
| β-strand | 69-70 | 2 | 3 |
| α-helix | 71-87 | 17 | |
Chain C: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-19 | 17 | |
| β-strand | 28 | 1 | 4 |
| α-helix | 30-40 | 11 | |
| α-helix | 46-48 | 3 | |
| α-helix | 51-61 | 11 | |
| β-strand | 69 | 1 | 4 |
| α-helix | 71-87 | 17 | |
Chain D: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-19 | 17 | |
| β-strand | 28 | 1 | 5 |
| α-helix | 30-40 | 11 | |
| α-helix | 46-48 | 3 | |
| α-helix | 51-61 | 11 | |
| β-strand | 69 | 1 | 5 |
| α-helix | 71-85 | 15 | |
Chain P: 1 helix, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| β-strand | 58 | 1 | 1 |
| α-helix | 60-62 | 3 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Receptor for advanced glycation endproducts-derived peptide (W61) | P | protein | 15 | synthetic construct | Q15109 (AlphaFold model) |
| Protein S100-B | A, B, C, D | protein | 92 | Homo sapiens | P04271 (AlphaFold model) |
Sequence of entity 1 (P), FASTA
>4XYN_1 Receptor for advanced glycation endproducts-derived peptide (W61) (chains P)
NTGRTEAWKVLSPQG
Sequence of entity 2 (A, B, C, D), FASTA
>4XYN_2 Protein S100-B (chains A, B, C, D)
MSELEKAMVALIDVFHQYSGREGDKHKLKKSELKELINNELSHFLEEIKEQEVVDKVMET
LDNDGDGECDFQEFMAFVAMVTTACHEFFEHE
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| CA | Calcium ion | Ca | 8 |
Primary citation
Structural insights into the binding of the human receptor for advanced glycation end products (RAGE) by S100B, as revealed by an S100B-RAGE-derived peptide complex. Jensen, J.L., Indurthi, V.S., Neau, D.B. et al. Acta Crystallogr D Biol Crystallogr (2015) 71:1176-1183. DOI 10.1107/S1399004715004216 · PubMed
Other PDB entries of the same protein (UniProt Q15109 (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
- 3O3U 1.5 Å, Crystal Structure of Human Receptor for Advanced Glycation Endproducts (RAGE)
- 6XQ1 1.51 Å, Receptor for Advanced Glycation End Products VC1 domain in complex with…
- 6XQ3 1.71 Å, Receptor for Advanced Glycation End Products VC1 domain in complex with…
- 6XQ5 1.8 Å, Receptor for Advanced Glycation End Products VC1 domain in complex with Fragment 1
- 6XQ7 1.8 Å, Receptor for Advanced Glycation End Products VC1 domain in complex with Fragment 5
- 6XQ8 1.82 Å, Receptor for Advanced Glycation End Products VC1 domain in complex with Fragments 1 & 11
- 3CJJ 1.85 Å, Crystal structure of human rage ligand-binding domain
- 6XQ6 1.9 Å, Receptor for Advanced Glycation End Products VC1 domain in complex with Fragment 11
- 7LML 2.15 Å, Receptor for Advanced Glycation End Products VC1 domain in complex with…
- 4P2Y 2.3 Å, Crystal structure of the human RAGE ectodomain (fragment VC1C2) in complex with mouse…
- 6XQ9 2.3 Å, Receptor for Advanced Glycation End Products VC1 domain in complex with Fragments 1 & 13
Browse structure collections
About this viewer
MolViewer shows 4XYN 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.