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Crystal structure of the Fab fragment of the human HIV-1 neutralizing antibody PGZL1.H4K3 in complex with its mper peptide epitope (region 671-683 of HIV-1 GP41).

Analyse Crystal structure of the Fab fragment of the human HIV-1 neutralizing antibody… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6O3L
Type: protein
Length: 905 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: PGZL1.H4K3 light chain; PGZL1.H4K3 heavy chain; Mper peptide, region 671-683 of HIV-1 GP41
Ligands: PO4
Pockets: 9 · best druggability 0.72

Structure

x-ray diffraction · 4 distinct chains · 11% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L, B	PGZL1.H4K3 light chain	protein	214	7% helix, 50% strand	—
H	PGZL1.H4K3 heavy chain	protein	223	11% helix, 53% strand	—
A	PGZL1.H4K3 heavy chain	protein	222	10% helix, 53% strand	—
D, E	Mper peptide, region 671-683 of HIV-1 GP41	protein	16	88% helix, 0% strand	—

Ligands and binding sites

PO4 · Phosphate ion · ion · 6 copies · chains H, L, B, A
GOL · Glycerol · additive · 5 copies · chains L, H, A, B, E

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

Pockets

9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	964	0.72	0.76	99	empty
2	612	0.64	0.75	72	empty
3	237	0.53	0.76	38	empty
4	152	0.46	0.76	35	empty
5	96	0.44	0.79	19	GOL

Interfaces

8 interfaces between chains.

B–A · 1914 Å² buried · 14 hydrogen bonds · protein-protein
L–H · 1871 Å² buried · 19 hydrogen bonds · protein-protein
H–D · 623 Å² buried · 9 hydrogen bonds · protein-protein
A–E · 601 Å² buried · 7 hydrogen bonds · protein-protein
L–B · 560 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

6O3L · Crystal structure of the Fab fragment of the human HIV-1 neutralizing antibody PGZL1.H4K3… · 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 6O3L · PDBe 6O3L

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