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Crystal structure of mouse prion protein complexed with promazine

Analyse Crystal structure of mouse prion protein complexed with promazine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4MA7
Type: protein
Length: 541 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Major prion protein; POM1 heavy chain; POM1 light chain
UniProt: P04925
Ligands: P2Z
Pockets: 4 · best druggability 0.59

Structure

x-ray diffraction · 3 distinct chains · 17% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Major prion protein	protein	110	59% helix, 5% strand	P04925
H	POM1 heavy chain	protein	218	7% helix, 52% strand	—
L	POM1 light chain	protein	213	6% helix, 52% strand	—

Ligands and binding sites

P2Z · Promazine · ligand · chains A

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

Pockets

4 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	437	0.59	0.75	62	empty
2	215	0.52	0.77	33	empty
3	91	0.34	0.74	16	empty
4	60	0.29	0.74	18	empty

Interfaces

3 interfaces between chains.

H–L · 1755 Å² buried · 17 hydrogen bonds · protein-protein
A–H · 429 Å² buried · 9 hydrogen bonds · protein-protein
A–L · 267 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

4MA7 · Crystal structure of mouse prion protein complexed with Promazine · the same entry in another collection · chain A against A, TM-score 1.00
P04925 · AlphaFold monomer V2.0 prediction for major prion protein (P04925) · a predicted model of the same protein · chain A against A, TM-score 0.94

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 P04925
Elsewhere: RCSB PDB 4MA7 · PDBe 4MA7 · UniProt P04925

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