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Crystal structure of LN01 Fab in complex with an HIV-1 GP41 peptide

Analyse Crystal structure of LN01 Fab in complex with an HIV-1 GP41 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6SNE
Type: protein
Length: 1,913 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Envelope glycoprotein GP160; LN01 light chain; LN01 heavy chain
UniProt: Q74599
Ligands: PC, NAG
Pockets: 14 · best druggability 0.78

Structure

x-ray diffraction · 9 distinct chains · 17% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
O	Envelope glycoprotein GP160	protein	39	74% helix, 0% strand	Q74599
A, E	LN01 light chain	protein	210	7% helix, 51% strand	—
B	LN01 heavy chain	protein	223	7% helix, 49% strand	—
F, H, D	LN01 heavy chain	protein	229	9% helix, 49% strand	—
N	Envelope glycoprotein GP160	protein	41	85% helix, 0% strand	Q74599
L	LN01 light chain	protein	213	7% helix, 51% strand	—
P	Envelope glycoprotein GP160	protein	44	77% helix, 0% strand	Q74599
C	LN01 light chain	protein	212	7% helix, 51% strand	—
J	Envelope glycoprotein GP160	protein	34	82% helix, 0% strand	Q74599

Ligands and binding sites

PC · Phosphocholine · ligand · 10 copies · chains O, A, B, F, N, E, L, H, P, C, D, J
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, E, L, C

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

Pockets

14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	900	0.78	0.80	68	PC
2	730	0.66	0.75	64	empty
3	575	0.63	0.75	53	empty
4	597	0.63	0.74	52	empty
5	553	0.61	0.74	49	empty

Interfaces

24 interfaces between chains.

E–F · 2066 Å² buried · 13 hydrogen bonds · protein-protein
C–D · 2016 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 1929 Å² buried · 13 hydrogen bonds · protein-protein
L–H · 1902 Å² buried · 11 hydrogen bonds · protein-protein
H–P · 528 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

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

Compared structures

6SNE · crystal structure of LN01 Fab in complex with an HIV-1 gp41 peptide · the same entry in another collection · chain O against O, 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 Q74599
Elsewhere: RCSB PDB 6SNE · PDBe 6SNE · UniProt Q74599

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