MolNFT v1 · #116667 · protein

Crystal structure of calcium-loaded S100B bound to SBI4225

5DKN · Protein S100-B: “Crystal structure of calcium-loaded S100B bound to SBI4225”. X-ray diffraction, 2 ligands (B7I, CA), 2 pockets (best druggability 0.34). MolNFT v1 #116667 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 5DKN
Type: protein
Length: 91 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein S100-B
UniProt: P02638
Ligands: B7I, CA
Pockets: 2 · best druggability 0.34

Structure

x-ray diffraction · 1 distinct chain · 60% helix, 2% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein S100-B	protein	91	60% helix, 2% strand	P02638

Ligands and binding sites

B7I · 2,2'-[heptane-1,7-diylbis(oxybenzene-4,1-diyl)]bis(1H-imidazole) · ligand · chains A
CA · Calcium ion · metal · 2 copies · chains A

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

Pockets

2 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	70	0.34	0.75	13	empty
2	66	0.29	0.73	17	empty

Compared structures

5DKN · Crystal Structure of Calcium-loaded S100B bound to SBi4225 · the same entry in another collection · chain A against A, TM-score 1.00
P02638 · AlphaFold monomer V2.0 prediction for protein S100-B (P02638) · a predicted model of the same protein · chain A against A, TM-score 0.95

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 P02638
Elsewhere: RCSB PDB 5DKN · PDBe 5DKN · UniProt P02638

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