MolNFT v1 · #63882 · protein

Crystal structure of HIV-1 neutralizing human Fab Z13E1 in complex with a 12-residue peptide containing the Z13E1 epitope on GP41

3FN0: “Crystal structure of HIV-1 neutralizing human Fab Z13E1 in complex with a 12-residue peptide containing the…”. X-ray diffraction, 2 pockets (best druggability 0.54). MolNFT v1 #63882 on GenesisL1: 3D structure, binding sites and…

PDB: 3FN0
Type: protein
Length: 439 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab Z13E1; Envelope polyprotein GP160
Pockets: 2 · best druggability 0.54

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Fab Z13E1	protein	209	6% helix, 51% strand	—
H	Fab Z13E1	protein	221	6% helix, 53% strand	—
P	Envelope polyprotein GP160	protein	9	0% helix, 0% strand	—

Pockets

2 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	353	0.54	0.74	48	empty
2	53	0.47	0.86	22	empty

Interfaces

3 interfaces between chains.

L–H · 1877 Å² buried · 20 hydrogen bonds · protein-protein
H–P · 528 Å² buried · 9 hydrogen bonds · protein-protein
L–P · 37 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

3FN0 · Crystal structure of HIV-1 neutralizing human Fab Z13e1 in complex with a 12-residue… · 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 3FN0 · PDBe 3FN0

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