MolNFT v1 · #182664 · protein

Crystal structure of the F240 antibody fragment bound to the HIV-1 GP41 immunodominant region

7N05 · Fab F240 heavy chain: “Crystal structure of the F240 antibody fragment bound to the HIV-1 GP41 immunodominant region”. X-ray diffraction, 1 ligand (ACE), 5 pockets (best druggability 0.51). MolNFT v1 #182664 on GenesisL1: 3D…

PDB: 7N05
Type: protein
Length: 454 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab F240 heavy chain; Fab F240 light chain; HIV-1 GP41 immunodominant region
Ligands: ACE
Pockets: 5 · best druggability 0.51

Structure

x-ray diffraction · 3 distinct chains · 7% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Fab F240 heavy chain	protein	221	8% helix, 56% strand	—
L	Fab F240 light chain	protein	218	6% helix, 51% strand	—
E	HIV-1 GP41 immunodominant region	protein	15	20% helix, 20% strand	—

Ligands and binding sites

ACE · Acetyl group · ligand · chains H, E
GOL · Glycerol · additive · 2 copies · chains H, L
ACT · Acetate ion · additive · chains H, L

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

Pockets

5 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	271	0.51	0.75	40	ACT
2	103	0.35	0.74	19	empty
3	107	0.35	0.73	25	empty
4	102	0.33	0.72	18	empty
5	59	0.25	0.72	18	empty

Interfaces

3 interfaces between chains.

H–L · 1754 Å² buried · 19 hydrogen bonds · protein-protein
H–E · 443 Å² buried · 14 hydrogen bonds · protein-protein
L–E · 266 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide, 1 covalent (disulfide, covalent ligand).

Compared structures

7N05 · Crystal structure of the F240 antibody fragment bound to the HIV-1 gp41 immunodominant… · 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
Elsewhere: RCSB PDB 7N05 · PDBe 7N05

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.