Research workbench

Crystal structure of anti-amyloid beta Fab WO2 (P21, formb)

Analyse Crystal structure of anti-amyloid beta Fab WO2 (P21, formb) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3BKC
Type: protein
Length: 442 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: WO2 IGG2A Fab fragment light chain kappa; WO2 IGG2A Fab fragment heavy chain
Ligands: NA
Pockets: 5 · best druggability 0.54

Structure

x-ray diffraction · 2 distinct chains · 7% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	WO2 IGG2A Fab fragment light chain kappa	protein	218	6% helix, 51% strand	—
H	WO2 IGG2A Fab fragment heavy chain	protein	224	8% helix, 52% strand	—

Ligands and binding sites

NA · Sodium ion · metal · chains H

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

Pockets

5 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	183	0.54	0.79	24	empty
2	337	0.52	0.73	32	empty
3	74	0.32	0.74	20	empty
4	59	0.30	0.75	14	empty
5	66	0.28	0.73	16	empty

Interfaces

1 interface between chains.

L–H · 2002 Å² buried · 23 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

3BKC · Crystal structure of anti-amyloid beta FAB WO2 (P21, FormB) · the same entry in another collection · chain L against L, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 3BKC · PDBe 3BKC

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