MolNFT v1 · #151230 · protein

Mouse prion protein in complex with nanobody 484

6HHD · Major prion protein: “Mouse prion protein in complex with nanobody 484”. X-ray diffraction, 3 ligands (NA, SO4, CL), 2 pockets (best druggability 0.44). MolNFT v1 #151230 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6HHD
Type: protein
Length: 464 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Major prion protein; Nanobody 484
UniProt: P04925
Ligands: NA, SO4, CL
Pockets: 2 · best druggability 0.44

Structure

x-ray diffraction · 4 distinct chains · 30% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Major prion protein	protein	108	56% helix, 10% strand	P04925
B	Nanobody 484	protein	124	7% helix, 45% strand	—
C	Major prion protein	protein	107	55% helix, 10% strand	P04925
D	Nanobody 484	protein	125	7% helix, 45% strand	—

Ligands and binding sites

NA · Sodium ion · metal · chains C, D
SO4 · Sulfate ion · ion · 4 copies · chains B, C, D
CL · Chloride ion · ion · 3 copies · chains B, D
GOL · Glycerol · additive · chains C

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	123	0.44	0.77	22	empty
2	104	0.42	0.77	20	empty

Interfaces

4 interfaces between chains.

C–D · 691 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 685 Å² buried · 8 hydrogen bonds · protein-protein
B–C · 291 Å² buried · 3 hydrogen bonds · protein-protein
A–D · 276 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

6HHD · Mouse Prion Protein in complex with Nanobody 484 · 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 C 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 6HHD · PDBe 6HHD · UniProt P04925

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.