Research workbench

X-ray structure of bovine SC0067,CA(2+)-S100B

Analyse X-ray structure of bovine SC0067,CA(2+)-S100B in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3LK0
Type: protein
Length: 357 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein S100-B
UniProt: P02638
Ligands: Z80, CA
Pockets: 4 · best druggability 0.39

Structure

x-ray diffraction · 2 distinct chains · 64% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Protein S100-B	protein	89	64% helix, 4% strand	P02638
D	Protein S100-B	protein	90	64% helix, 2% strand	P02638

Ligands and binding sites

Z80 · 3-(2-chloro-10H-phenothiazin-10-yl)-N,N-dimethylpropan-1-amine · ligand · 2 copies · chains A, B, D
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

4 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	73	0.39	0.78	12	empty
2	88	0.39	0.76	14	empty
3	72	0.35	0.77	14	empty
4	58	0.33	0.77	10	empty

Interfaces

2 interfaces between chains.

A–B · 1533 Å² buried · 22 hydrogen bonds · protein-protein
A–C · 339 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

3LK0 · X-ray structure of bovine SC0067,Ca(2+)-S100B · 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 D 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 3LK0 · PDBe 3LK0 · UniProt P02638

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