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Fab fragment of an antibody selective for alpha-1-antitrypsin in the native conformation

Analyse Fab fragment of an antibody selective for alpha-1-antitrypsin in the native… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6GXX
Type: protein
Length: 435 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab 1D9 heavy chain; Fab 1D9 light chain
Ligands: MG
Pockets: 3 · best druggability 0.55

Structure

x-ray diffraction · 2 distinct chains · 7% helix, 54% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Fab 1D9 heavy chain	protein	219	7% helix, 55% strand	—
L	Fab 1D9 light chain	protein	216	6% helix, 52% strand	—

Ligands and binding sites

MG · Magnesium ion · metal · chains L

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	301	0.55	0.76	42	MG
2	79	0.38	0.77	19	empty
3	85	0.34	0.74	22	empty

Interfaces

1 interface between chains.

H–L · 1814 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

6GXX · Fab fragment of an antibody selective for alpha-1-antitrypsin in the native conformation · 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 6GXX · PDBe 6GXX

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