MolNFT v1 · #93623 · protein

Structure of POM1 Fab fragment complexed with mouse prpc fragment 120- 230

4H88 · Major prion protein: “Structure of POM1 Fab fragment complexed with mouse prpc fragment 120- 230”. X-ray diffraction, 1 ligand (NA), 5 pockets (best druggability 0.58). MolNFT v1 #93623 on GenesisL1: 3D structure, binding sites and…

PDB: 4H88
Type: protein
Length: 533 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Major prion protein; POM1 Fab chain H; POM1 Fab chain L
UniProt: P04925
Ligands: NA
Pockets: 5 · best druggability 0.58

Structure

x-ray diffraction · 3 distinct chains · 17% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Major prion protein	protein	102	61% helix, 4% strand	P04925
H	POM1 Fab chain H	protein	218	8% helix, 51% strand	—
L	POM1 Fab chain L	protein	213	6% helix, 50% 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	426	0.58	0.75	63	empty
2	144	0.43	0.75	29	empty
3	80	0.31	0.73	16	empty
4	57	0.29	0.74	18	empty
5	53	0.26	0.74	13	empty

Interfaces

3 interfaces between chains.

H–L · 1714 Å² buried · 14 hydrogen bonds · protein-protein
A–H · 433 Å² buried · 9 hydrogen bonds · protein-protein
A–L · 269 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

4H88 · Structure of POM1 FAB fragment complexed with mouse PrPc Fragment 120-230 · 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 0.95

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 P04925
Elsewhere: RCSB PDB 4H88 · PDBe 4H88 · UniProt P04925

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