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A non-self sugar mimic of the HIV glycan shield shows enhanced antigenicity

Analyse A non-self sugar mimic of the HIV glycan shield shows enhanced antigenicity in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3OB0
Type: protein
Length: 864 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab 2G12, light chain; Fab 2G12, heavy chain
Ligands: YYH, MAN
Pockets: 10 · best druggability 0.75

Structure

x-ray diffraction · 4 distinct chains · 6% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Fab 2G12, light chain	protein	212	6% helix, 53% strand	—
H	Fab 2G12, heavy chain	protein	220	7% helix, 51% strand	—
K	Fab 2G12, light chain	protein	213	6% helix, 53% strand	—
M	Fab 2G12, heavy chain	protein	219	4% helix, 52% strand	—

Ligands and binding sites

YYH · 7-deoxy-L-glycero-alpha-D-manno-heptopyranose · ligand · 2 copies · chains L, H, K, M
MAN · alpha-D-mannopyranose · sugar · 6 copies · chains H, L, M, K

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

Pockets

10 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	1021	0.75	0.78	97	empty
2	546	0.64	0.76	52	empty
3	426	0.64	0.78	46	empty
4	119	0.37	0.74	25	empty
5	97	0.36	0.75	19	empty

Interfaces

6 interfaces between chains.

H–M · 988 Å² buried · 15 hydrogen bonds · protein-protein
L–H · 967 Å² buried · 10 hydrogen bonds · protein-protein
K–M · 954 Å² buried · 12 hydrogen bonds · protein-protein
H–K · 952 Å² buried · 8 hydrogen bonds · protein-protein
L–M · 911 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

3OB0 · A non-self sugar mimic of the HIV glycan shield shows enhanced antigenicity · 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 3OB0 · PDBe 3OB0

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