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An anti-urokinase plasminogen activator receptor (upar) antibody: crystal structure and binding epitope

Analyse An anti-urokinase plasminogen activator receptor (upar) antibody: crystal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2FAT
Type: protein
Length: 426 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab atn-615, light chain; Fab atn-615, heavy chain
Pockets: 5 · best druggability 0.54

Structure

x-ray diffraction · 2 distinct chains · 6% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Fab atn-615, light chain	protein	212	6% helix, 51% strand	—
H	Fab atn-615, heavy chain	protein	214	6% helix, 53% strand	—

Pockets

5 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	340	0.54	0.74	40	empty
2	56	0.45	0.84	20	empty
3	72	0.30	0.74	19	empty
4	68	0.28	0.73	15	empty
5	68	0.28	0.72	17	empty

Interfaces

1 interface between chains.

L–H · 1795 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

2FAT · An anti-urokinase plasminogen activator receptor (UPAR) antibody: Crystal structure and… · 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 2FAT · PDBe 2FAT

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