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4-4-20 Fab fragment

Analyse 4-4-20 Fab fragment in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1FLR
Type: protein
Length: 435 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 4-4-20 (IG*G2A=KAPPA=) Fab fragment
UniProt: P01865
Ligands: FLU
Pockets: 5 · best druggability 0.56

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	4-4-20 (IG*G2A=KAPPA=) Fab fragment	protein	219	6% helix, 49% strand	—
H	4-4-20 (IG*G2A=KAPPA=) Fab fragment	protein	216	8% helix, 50% strand	P01865

Ligands and binding sites

FLU · 2-(6-hydroxy-3-oxo-3H-xanthen-9-yl)-benzoic acid · ligand · chains L, 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	417	0.56	0.73	41	empty
2	141	0.51	0.79	19	FLU
3	133	0.42	0.75	25	empty
4	61	0.33	0.77	17	empty
5	61	0.28	0.74	11	empty

Interfaces

1 interface between chains.

L–H · 1979 Å² buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

1FLR · 4-4-20 Fab fragment · the same entry in another collection · chain L against L, TM-score 1.00
P01865 · AlphaFold monomer V2.0 prediction for ig gamma-2A chain C region, membrane-bound form… · a predicted model of the same protein · chain H against A, TM-score 0.48

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P01865
Elsewhere: RCSB PDB 1FLR · PDBe 1FLR · UniProt P01865

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