Research workbench

Fab fragment

Analyse Fab fragment in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1YUH
Type: protein
Length: 858 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 88C6/12 Fab (light chain); 88C6/12 Fab (heavy chain)
Ligands: NP
Pockets: 8 · best druggability 0.70

Structure

x-ray diffraction · 2 distinct chains · 5% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L, A	88C6/12 Fab (light chain)	protein	211	7% helix, 45% strand	—
H, B	88C6/12 Fab (heavy chain)	protein	218	3% helix, 42% strand	—

Ligands and binding sites

NP · 4-hydroxy-3-nitrophenylacetyl-epsilon-aminocaproic acid · ligand · 2 copies · chains L, H, A, B

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

Pockets

8 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	806	0.70	0.76	70	empty
2	731	0.65	0.74	66	empty
3	125	0.44	0.78	24	empty
4	98	0.37	0.75	18	empty
5	91	0.35	0.74	25	empty

Interfaces

2 interfaces between chains.

A–B · 2218 Å² buried · 17 hydrogen bonds · protein-protein
L–H · 2067 Å² buried · 20 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

1YUH · Fab fragment · 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 1YUH · PDBe 1YUH

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