MolNFT v1 · #121532 · protein

Crystal structure of calcium-free human S100Z

5HYD · Protein S100-Z: “Crystal structure of calcium-free human S100Z”. X-ray diffraction, 3 pockets (best druggability 0.75). MolNFT v1 #121532 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5HYD
Type: protein
Length: 381 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein S100-Z
UniProt: Q8WXG8
Pockets: 3 · best druggability 0.75

Structure

x-ray diffraction · 3 distinct chains · 69% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Protein S100-Z	protein	96	73% helix, 6% strand	Q8WXG8
B	Protein S100-Z	protein	95	67% helix, 6% strand	Q8WXG8
C	Protein S100-Z	protein	94	66% helix, 6% strand	Q8WXG8

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	639	0.75	0.81	60	empty
2	95	0.43	0.79	17	empty
3	89	0.41	0.77	13	empty

Interfaces

6 interfaces between chains.

C–D · 1179 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 1097 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 827 Å² buried · 3 hydrogen bonds · protein-protein
A–D · 296 Å² buried · 7 hydrogen bonds · protein-protein
B–D · 214 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

5HYD · Crystal structure of calcium-free human S100Z · the same entry in another collection · chain A against A, TM-score 1.00
Q8WXG8 · AlphaFold monomer V2.0 prediction for protein S100-Z (Q8WXG8) · a predicted model of the same protein · chain C against A, TM-score 0.64

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 Q8WXG8
Elsewhere: RCSB PDB 5HYD · PDBe 5HYD · UniProt Q8WXG8

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