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Crystal structure of broad neutralizing antibody 10E8 with long epitope bound

Analyse Crystal structure of broad neutralizing antibody 10E8 with long epitope bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5GHW
Type: protein
Length: 465 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab 10E8 heavy chain; Fab 10E8 light chain; Endogenous retrovirus group K member 8 env…
UniProt: G3DED6
Ligands: PO4
Pockets: 3 · best druggability 0.68

Structure

x-ray diffraction · 3 distinct chains · 11% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Fab 10E8 heavy chain	protein	233	6% helix, 51% strand	—
L	Fab 10E8 light chain	protein	211	8% helix, 50% strand	—
P	Endogenous retrovirus group K member 8 env polyprotein	protein	21	81% helix, 0% strand	G3DED6

Ligands and binding sites

PO4 · Phosphate ion · ion · 7 copies · chains H, L

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	828	0.68	0.75	73	empty
2	89	0.42	0.79	20	empty
3	103	0.40	0.76	25	empty

Interfaces

3 interfaces between chains.

H–L · 2204 Å² buried · 19 hydrogen bonds · protein-protein
H–P · 707 Å² buried · 10 hydrogen bonds · protein-protein
L–P · 98 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

5GHW · Crystal structure of broad neutralizing antibody 10E8 with long epitope bound · 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
Every structure of UniProt G3DED6
Elsewhere: RCSB PDB 5GHW · PDBe 5GHW · UniProt G3DED6

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