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Structure of PG16, an antibody with broad and potent neutralization of HIV-1

Analyse Structure of PG16, an antibody with broad and potent neutralization of HIV-1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3LRS
Type: protein
Length: 1,734 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pg-16 heavy chain Fab; Pg-16 light chain Fab
Ligands: NAG
Pockets: 19 · best druggability 0.70

Structure

x-ray diffraction · 5 distinct chains · 8% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Pg-16 heavy chain Fab	protein	220	7% helix, 53% strand	—
L, B, D, F	Pg-16 light chain Fab	protein	211	7% helix, 51% strand	—
A	Pg-16 heavy chain Fab	protein	221	7% helix, 54% strand	—
C	Pg-16 heavy chain Fab	protein	228	9% helix, 52% strand	—
E	Pg-16 heavy chain Fab	protein	221	8% helix, 52% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains L, B, D, F

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

Pockets

19 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	937	0.70	0.75	100	empty
2	831	0.69	0.76	74	empty
3	832	0.69	0.75	78	empty
4	826	0.66	0.73	73	empty
5	640	0.64	0.74	61	empty

Interfaces

13 interfaces between chains.

C–D · 1863 Å² buried · 19 hydrogen bonds · protein-protein
H–L · 1789 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 1777 Å² buried · 16 hydrogen bonds · protein-protein
E–F · 1772 Å² buried · 15 hydrogen bonds · protein-protein
H–F · 562 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide, 4 glycan (disulfide, N-glycosylation).

Compared structures

3LRS · Structure of PG16, an antibody with broad and potent neutralization of HIV-1 · 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 3LRS · PDBe 3LRS

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