Research workbench

Fab 7D6 bound to APOL1 BH3 like peptide

Analyse Fab 7D6 bound to APOL1 BH3 like peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7LFD
Type: protein
Length: 455 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Apolipoprotein L1 BH3 like peptide; Fab 7D6 heavy chain; Fab 7D6 light chain
UniProt: O14791
Ligands: NH4
Pockets: 4 · best druggability 0.64

Structure

x-ray diffraction · 3 distinct chains · 10% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Apolipoprotein L1 BH3 like peptide	protein	17	65% helix, 0% strand	O14791
H	Fab 7D6 heavy chain	protein	224	11% helix, 53% strand	—
L	Fab 7D6 light chain	protein	214	6% helix, 51% strand	—

Ligands and binding sites

NH4 · Ammonium ion · ion · chains H, L
GOL · Glycerol · additive · 3 copies · chains H, L
FLC · Citrate anion · additive · chains A, H
EOH · Ethanol · additive · chains H

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

Pockets

4 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	681	0.64	0.74	62	NH4
2	51	0.47	0.86	21	empty
3	83	0.36	0.75	19	GOL
4	57	0.28	0.74	21	empty

Interfaces

3 interfaces between chains.

H–L · 2051 Å² buried · 15 hydrogen bonds · protein-protein
A–H · 613 Å² buried · 11 hydrogen bonds · protein-protein
A–L · 394 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

7LFD · Fab 7D6 bound to ApoL1 BH3 like peptide · the same entry in another collection · chain L against L, TM-score 1.00
O14791 · AlphaFold monomer V2.0 prediction for apolipoprotein L1 (O14791) · a predicted model of the same protein · chain A against A, TM-score 0.65

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 O14791
Elsewhere: RCSB PDB 7LFD · PDBe 7LFD · UniProt O14791

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