MolNFT v1 · #111660 · protein

Crystal structure of deer prion protein complexed with POM1 Fab

4YXH · Major prion protein: “Crystal structure of deer prion protein complexed with POM1 Fab”. X-ray diffraction, 1 ligand (NA), 5 pockets (best druggability 0.57). MolNFT v1 #111660 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 4YXH
Type: protein
Length: 532 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: P47852
Ligands: NA
Pockets: 5 · best druggability 0.57

Structure

x-ray diffraction · 3 distinct chains · 17% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Major prion protein	protein	101	60% helix, 4% strand	P47852
H	POM1 Fab heavy chain	protein	218	7% helix, 52% strand	—
L	POM1 Fab light chain	protein	213	6% helix, 42% strand	—

Ligands and binding sites

NA · Sodium ion · metal · chains L

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

Pockets

5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	305	0.57	0.77	35	empty
2	398	0.57	0.75	54	empty
3	108	0.55	0.84	22	empty
4	69	0.52	0.86	15	empty
5	56	0.27	0.74	17	empty

Interfaces

3 interfaces between chains.

H–L · 1796 Å² buried · 13 hydrogen bonds · protein-protein
A–H · 421 Å² buried · 11 hydrogen bonds · protein-protein
A–L · 264 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

4YXH · Crystal structure of Deer prion protein complexed with POM1 FAB · the same entry in another collection · chain A against A, TM-score 1.00
P47852 · AlphaFold monomer V2.0 prediction for major prion protein (P47852) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 P47852
Elsewhere: RCSB PDB 4YXH · PDBe 4YXH · UniProt P47852

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