Research workbench

Crossreactive binding of a circularized peptide to an anti-tgfalpha antibody Fab-fragment

Analyse Crossreactive binding of a circularized peptide to an anti-tgfalpha antibody… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1E4W
Type: protein
Length: 434 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: TAB2; Cyclic peptide
Ligands: NI, CL
Pockets: 4 · best druggability 0.52

Structure

x-ray diffraction · 3 distinct chains · 6% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	TAB2	protein	213	7% helix, 50% strand	—
L	TAB2	protein	214	6% helix, 51% strand	—
P	Cyclic peptide	protein	7	0% helix, 0% strand	—

Ligands and binding sites

NI · Nickel (II) ion · metal · chains L
CL · Chloride ion · ion · chains H, P

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	304	0.52	0.74	49	empty
2	117	0.41	0.76	22	empty
3	99	0.37	0.75	17	empty
4	66	0.29	0.74	17	empty

Interfaces

3 interfaces between chains.

H–L · 1684 Å² buried · 14 hydrogen bonds · protein-protein
L–P · 325 Å² buried · 3 hydrogen bonds · protein-protein
H–P · 222 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

1E4W · crossreactive binding of a circularized peptide to an anti-TGFalpha antibody Fab-fragment · the same entry in another collection · chain H against H, 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 1E4W · PDBe 1E4W

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