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Crystal structure of a Fab

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

PDB: 4NKI
Type: protein
Length: 433 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab light chain; Fab heavy chain
Pockets: 3 · best druggability 0.52

Structure

x-ray diffraction · 2 distinct chains · 7% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Fab light chain	protein	221	7% helix, 51% strand	—
L	Fab heavy chain	protein	212	7% helix, 50% strand	—

Ligands and binding sites

EDO · 1,2-ethanediol · additive · 2 copies · chains H

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

Pockets

3 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	329	0.52	0.73	45	EDO
2	213	0.49	0.75	33	empty
3	111	0.37	0.74	28	empty

Interfaces

1 interface between chains.

H–L · 1764 Å² buried · 20 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

4NKI · Crystal structure of a Fab · 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 4NKI · PDBe 4NKI

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