MolNFT v1 · #116670 · protein

Crystal structure of calcium-loaded S100B bound to SBI4214

5DKQ · Protein S100-B: “Crystal structure of calcium-loaded S100B bound to SBI4214”. X-ray diffraction, 2 ligands (5D0, CA), 2 pockets (best druggability 0.36). MolNFT v1 #116670 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 5DKQ
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: 5D0, CA
Pockets: 2 · best druggability 0.36

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

5D0 · 2,2'-[pentane-1,5-diylbis(oxybenzene-4,1-diyl)]di-1,4,5,6-tetrahydropyrimidine · 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	64	0.36	0.77	13	empty
2	61	0.31	0.74	15	empty

Compared structures

5DKQ · Crystal Structure of Calcium-loaded S100B bound to SBi4214 · 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 5DKQ · PDBe 5DKQ · UniProt P02638

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