MolNFT v1 · #110499 · protein

X-ray structure of CA(2+)-S100B with human rage-derived W61 peptide

4XYN · Receptor for advanced glycation endproducts-derived peptide…: “X-ray structure of CA(2+)-S100B with human rage-derived W61 peptide”. X-ray diffraction, 1 ligand (CA), 3 pockets (best druggability 0.46). MolNFT v1 #110499 on…

PDB: 4XYN
Type: protein
Length: 369 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Receptor for advanced glycation endproducts-derived peptide (W61); Protein S100-B
UniProt: P04271
Ligands: CA
Pockets: 3 · best druggability 0.46

Structure

x-ray diffraction · 4 distinct chains · 62% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
P	Receptor for advanced glycation endproducts-derived peptide (W61)	protein	9	33% helix, 11% strand	—
A	Protein S100-B	protein	90	64% helix, 3% strand	P04271
B, C	Protein S100-B	protein	91	62% helix, 4% strand	P04271
D	Protein S100-B	protein	88	61% helix, 2% strand	P04271

Ligands and binding sites

CA · Calcium ion · metal · 8 copies · chains A, B, C, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	213	0.46	0.73	24	empty
2	168	0.41	0.73	25	empty
3	101	0.33	0.72	19	empty

Interfaces

6 interfaces between chains.

A–B · 1521 Å² buried · 12 hydrogen bonds · protein-protein
C–D · 1452 Å² buried · 12 hydrogen bonds · protein-protein
P–A · 489 Å² buried · 3 hydrogen bonds · protein-protein
B–D · 95 Å² buried · 1 hydrogen bond · protein-protein
A–C · 56 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

4XYN · X-ray structure of Ca(2+)-S100B with human RAGE-derived W61 peptide · the same entry in another collection · chain D against D, TM-score 1.00
P04271 · AlphaFold monomer V2.0 prediction for protein S100-B (P04271) · a predicted model of the same protein · chain A against A, TM-score 0.97

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P04271
Elsewhere: RCSB PDB 4XYN · PDBe 4XYN · UniProt P04271

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