MolNFT v1 · #111648 · protein

Crystal structure of bovine prion protein complexed with POM1 Fab

4YX2 · Major prion protein: “Crystal structure of bovine prion protein complexed with POM1 Fab”. X-ray diffraction, 4 pockets (best druggability 0.55). MolNFT v1 #111648 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4YX2
Type: protein
Length: 528 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Major prion protein; POM1 Fab heavy chain; POM1 Fab light chain
UniProt: P10279
Pockets: 4 · best druggability 0.55

Structure

x-ray diffraction · 3 distinct chains · 17% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Major prion protein	protein	101	60% helix, 4% strand	P10279
H	POM1 Fab heavy chain	protein	214	8% helix, 51% strand	—
L	POM1 Fab light chain	protein	213	5% helix, 49% strand	—

Pockets

4 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	390	0.55	0.74	45	empty
2	93	0.36	0.75	22	empty
3	95	0.34	0.74	18	empty
4	58	0.29	0.74	17	empty

Interfaces

3 interfaces between chains.

H–L · 1784 Å² buried · 15 hydrogen bonds · protein-protein
A–H · 420 Å² buried · 10 hydrogen bonds · protein-protein
A–L · 255 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

4YX2 · Crystal structure of Bovine prion protein complexed with POM1 FAB · the same entry in another collection · chain A against A, TM-score 1.00
P10279 · AlphaFold monomer V2.0 prediction for major prion protein (P10279) · 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 P10279
Elsewhere: RCSB PDB 4YX2 · PDBe 4YX2 · UniProt P10279

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