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Crystal structure of Fab DEL2D1, a deletion variant of anti-influenza antibody 2D1

Analyse Crystal structure of Fab DEL2D1, a deletion variant of anti-influenza antibody… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3QHF
Type: protein
Length: 441 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Human monoclonal antibody DEL2D1, Fab heavy chain; Human monoclonal antibody DEL2D1, Fab…
Pockets: 7 · best druggability 0.60

Structure

x-ray diffraction · 2 distinct chains · 7% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Human monoclonal antibody DEL2D1, Fab heavy chain	protein	226	8% helix, 52% strand	—
L	Human monoclonal antibody DEL2D1, Fab light chain	protein	215	7% helix, 51% strand	—

Pockets

7 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	513	0.60	0.74	56	empty
2	150	0.50	0.78	33	empty
3	121	0.47	0.78	19	empty
4	64	0.41	0.81	20	empty
5	57	0.36	0.79	16	empty

Interfaces

1 interface between chains.

H–L · 1897 Å² buried · 18 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide, 2 modified (disulfide, cyclization).

Compared structures

3QHF · Crystal Structure of Fab del2D1, a deletion variant of anti-influenza antibody 2D1 · the same entry in another collection · chain H against H, TM-score 1.00

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 3QHF · PDBe 3QHF

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