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Fab structure of a neutralizing antibody L3 from an early subtype a HIV-1 infected patient

Analyse Fab structure of a neutralizing antibody L3 from an early subtype a HIV-1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4F58
Type: protein
Length: 1,733 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Light chain of Fab of a neutralizing antibody L3; Heavy chain of Fab of a neutralizing…
Ligands: SO4
Pockets: 14 · best druggability 0.66

Structure

x-ray diffraction · 4 distinct chains · 8% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L, M, N, O	Light chain of Fab of a neutralizing antibody L3	protein	213	7% helix, 50% strand	—
H	Heavy chain of Fab of a neutralizing antibody L3	protein	219	8% helix, 52% strand	—
I, K	Heavy chain of Fab of a neutralizing antibody L3	protein	221	8% helix, 49% strand	—
J	Heavy chain of Fab of a neutralizing antibody L3	protein	220	8% helix, 51% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 15 copies · chains L, H, I, M, N, J, O, K

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

Pockets

14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	691	0.66	0.75	75	empty
2	656	0.66	0.76	77	empty
3	545	0.63	0.75	62	empty
4	577	0.62	0.74	62	empty
5	231	0.49	0.75	37	SO4

Interfaces

7 interfaces between chains.

O–K · 1905 Å² buried · 15 hydrogen bonds · protein-protein
N–J · 1900 Å² buried · 14 hydrogen bonds · protein-protein
L–H · 1885 Å² buried · 13 hydrogen bonds · protein-protein
M–I · 1878 Å² buried · 15 hydrogen bonds · protein-protein
H–I · 305 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide (disulfide).

Compared structures

4F58 · Fab structure of a neutralizing antibody L3 from an early subtype A HIV-1 infected patient · 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
Elsewhere: RCSB PDB 4F58 · PDBe 4F58

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