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2F5 epitope scaffold elicited anti-HIV-1 monoclonal antibody 11F10 in complex with HIV-1 GP41

Analyse 2F5 epitope scaffold elicited anti-HIV-1 monoclonal antibody 11F10 in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3LEX
Type: protein
Length: 876 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 11F10 antibody heavy chain; 11F10 antibody light chain; Envelope glycoprotein GP41
UniProt: Q9IJQ0
Ligands: NH2
Pockets: 7 · best druggability 0.60

Structure

x-ray diffraction · 3 distinct chains · 6% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H, A	11F10 antibody heavy chain	protein	212	6% helix, 54% strand	—
L, B	11F10 antibody light chain	protein	219	7% helix, 51% strand	—
P, C	Envelope glycoprotein GP41	protein	7	0% helix, 0% strand	Q9IJQ0

Ligands and binding sites

NH2 · Amino group · ion · 2 copies · chains P, C

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

Pockets

7 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	523	0.60	0.74	51	empty
2	524	0.59	0.74	55	empty
3	190	0.51	0.77	26	empty
4	94	0.39	0.77	26	empty
5	103	0.39	0.76	26	empty

Interfaces

8 interfaces between chains.

H–L · 1935 Å² buried · 14 hydrogen bonds · protein-protein
A–B · 1935 Å² buried · 14 hydrogen bonds · protein-protein
L–B · 399 Å² buried · 8 hydrogen bonds · protein-protein
B–C · 326 Å² buried · 6 hydrogen bonds · protein-protein
L–P · 325 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

3LEX · 2F5 Epitope scaffold elicited anti-HIV-1 monoclonal antibody 11F10 in complex with 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
Every structure of UniProt Q9IJQ0
Elsewhere: RCSB PDB 3LEX · PDBe 3LEX · UniProt Q9IJQ0

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