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Structure of a human monoclonal antibody Fab fragment against GP41 of human immunodeficiency virus type I

Analyse Structure of a human monoclonal antibody Fab fragment against GP41 of human… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1DFB
Type: protein
Length: 441 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: IGG1-kappa 3D6 Fab (light chain); IGG1-kappa 3D6 Fab (heavy chain)
UniProt: P01857
Pockets: 4 · best druggability 0.54

Structure

x-ray diffraction · 2 distinct chains · 5% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	IGG1-kappa 3D6 Fab (light chain)	protein	212	4% helix, 50% strand	—
H	IGG1-kappa 3D6 Fab (heavy chain)	protein	229	7% helix, 49% strand	P01857

Pockets

4 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	161	0.54	0.80	30	empty
2	194	0.46	0.74	31	empty
3	91	0.36	0.75	18	empty
4	64	0.29	0.74	15	empty

Interfaces

1 interface between chains.

L–H · 1845 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

1DFB · Structure of a human monoclonal antibody Fab fragment against GP41 of human… · 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
Every structure of UniProt P01857
Elsewhere: RCSB PDB 1DFB · PDBe 1DFB · UniProt P01857

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