Research workbench

Solution NMR structure of S100B bound to the high-affinity target peptide trtk-12

Analyse Solution NMR structure of S100B bound to the high-affinity target peptide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1MWN
Type: protein
Length: 206 residues
Chains: 4
Method: solution nmr
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: S-100 protein, beta chain; F-actin capping protein alpha-1 subunit
UniProt: P04631, P52907
Ligands: CA
Pockets: 5 · best druggability 0.61

Structure

solution nmr · 2 distinct chains · 60% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	S-100 protein, beta chain	protein	91	63% helix, 4% strand	P04631
X, Y	F-actin capping protein alpha-1 subunit	protein	12	42% helix, 0% strand	P52907

Ligands and binding sites

CA · Calcium ion · metal · 4 copies · chains A, B

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

Pockets

5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	82	0.61	0.89	18	empty
2	79	0.58	0.87	18	empty
3	115	0.49	0.79	19	empty
4	103	0.48	0.80	20	empty
5	159	0.41	0.73	29	empty

Interfaces

3 interfaces between chains.

A–B · 1454 Å² buried · 3 hydrogen bonds · protein-protein
A–X · 544 Å² buried · 1 hydrogen bond · protein-protein
B–Y · 541 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

1MWN · Solution NMR structure of S100B bound to the high-affinity target peptide TRTK-12 · the same entry in another collection · chain A against A, TM-score 1.00
P04631 · AlphaFold monomer V2.0 prediction for protein S100-B (P04631) · a predicted model of the same protein · chain A against A, TM-score 0.83
P52907 · AlphaFold monomer V2.0 prediction for F-actin-capping protein subunit alpha-1 (P52907) · a predicted model of the same protein · chain X against A, TM-score 0.52

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 P04631
Every structure of UniProt P52907
Elsewhere: RCSB PDB 1MWN · PDBe 1MWN · UniProt P04631 · UniProt P52907

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