MolNFT v1 · #143128 · protein

Structure of POM6 Fab fragment complexed with mouse prpc

6AQ7 · Major prion protein: “Structure of POM6 Fab fragment complexed with mouse prpc”. X-ray diffraction, 1 ligand (TCE), 8 pockets (best druggability 0.63). MolNFT v1 #143128 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6AQ7
Type: protein
Length: 530 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Major prion protein; POM6 Fab heavy chain; POM6 Fab light chain
UniProt: P04925
Ligands: TCE
Pockets: 8 · best druggability 0.63

Structure

x-ray diffraction · 3 distinct chains · 17% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Major prion protein	protein	100	61% helix, 4% strand	P04925
H	POM6 Fab heavy chain	protein	214	7% helix, 54% strand	—
L	POM6 Fab light chain	protein	216	6% helix, 53% strand	—

Ligands and binding sites

TCE · 3,3',3''-phosphanetriyltripropanoic acid · ligand · chains H
GOL · Glycerol · additive · 2 copies · chains A, L

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

Pockets

8 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	618	0.63	0.74	56	empty
2	196	0.55	0.79	30	empty
3	180	0.50	0.77	25	empty
4	83	0.39	0.78	13	empty
5	73	0.36	0.77	14	empty

Interfaces

3 interfaces between chains.

H–L · 1671 Å² buried · 14 hydrogen bonds · protein-protein
A–H · 537 Å² buried · 13 hydrogen bonds · protein-protein
A–L · 375 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

6AQ7 · Structure of POM6 FAB fragment complexed with mouse PrPc · 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 0.97

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 P04925
Elsewhere: RCSB PDB 6AQ7 · PDBe 6AQ7 · UniProt P04925

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