MolNFT v1 · #184618 · protein

Crystal structure of TAP01 in complex with amyloid beta peptide

7OW1 · Amyloid-beta precursor protein: “Crystal structure of TAP01 in complex with amyloid beta peptide”. X-ray diffraction, 3 pockets (best druggability 0.45). MolNFT v1 #184618 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 7OW1
Type: protein
Length: 443 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Amyloid-beta precursor protein; TAP01 family antibody heavy chain; TAP01 family antibody…
UniProt: P05067
Pockets: 3 · best druggability 0.45

Structure

x-ray diffraction · 3 distinct chains · 8% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Amyloid-beta precursor protein	protein	10	0% helix, 20% strand	P05067
H	TAP01 family antibody heavy chain	protein	219	8% helix, 51% strand	—
K	TAP01 family antibody light chain	protein	214	7% helix, 49% strand	—

Ligands and binding sites

FLC · Citrate anion · additive · chains H, K

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

Pockets

3 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	192	0.45	0.74	31	empty
2	72	0.40	0.79	17	empty
3	88	0.36	0.75	17	empty

Interfaces

3 interfaces between chains.

H–K · 1987 Å² buried · 13 hydrogen bonds · protein-protein
A–H · 341 Å² buried · 9 hydrogen bonds · protein-protein
A–K · 284 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide, 1 modified (disulfide, cyclization).

Compared structures

7OW1 · Crystal Structure of TAP01 in complex with amyloid beta peptide · the same entry in another collection · chain K against K, TM-score 1.00
P05067 · AlphaFold monomer V2.0 prediction for amyloid-beta precursor protein (P05067) · a predicted model of the same protein · chain A against A, TM-score 0.54

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 P05067
Elsewhere: RCSB PDB 7OW1 · PDBe 7OW1 · UniProt P05067

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