MolNFT v1 · #80569 · protein

Fab-antibody complex

3U0T · Ponezumab lc Fab: “Fab-antibody complex”. X-ray diffraction, 13 pockets (best druggability 0.80). MolNFT v1 #80569 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3U0T
Type: protein
Length: 875 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ponezumab lc Fab; Ponezumab hc Fab; Amyloid beta A4 protein
UniProt: P05067
Pockets: 13 · best druggability 0.80

Structure

x-ray diffraction · 5 distinct chains · 6% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	Ponezumab lc Fab	protein	219	5% helix, 51% strand	—
D	Ponezumab hc Fab	protein	207	6% helix, 54% strand	—
E, F	Amyloid beta A4 protein	protein	11	0% helix, 0% strand	P05067
A	Ponezumab lc Fab	protein	218	6% helix, 51% strand	—
B	Ponezumab hc Fab	protein	209	7% helix, 52% strand	—

Pockets

13 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	492	0.80	0.87	60	empty
2	614	0.78	0.84	70	empty
3	221	0.51	0.76	34	empty
4	52	0.51	0.88	21	empty
5	75	0.40	0.78	17	empty

Interfaces

11 interfaces between chains.

C–D · 1780 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 1762 Å² buried · 12 hydrogen bonds · protein-protein
D–E · 456 Å² buried · 9 hydrogen bonds · protein-protein
B–F · 420 Å² buried · 9 hydrogen bonds · protein-protein
D–A · 371 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide (disulfide).

Compared structures

3U0T · Fab-antibody complex · the same entry in another collection · chain F against F, TM-score 1.00
P05067 · AlphaFold monomer V2.0 prediction for amyloid-beta precursor protein (P05067) · a predicted model of the same protein · chain F against A, TM-score 0.34

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 3U0T · PDBe 3U0T · UniProt P05067

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