Research workbench

Fab 3B6 bound to APOL1 ntd

Analyse Fab 3B6 bound to APOL1 ntd in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7LFA
Type: protein
Length: 1,058 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Apolipoprotein L1; Fab 3B6 heavy chain; Fab 3B6 light chain
UniProt: O14791
Ligands: CL
Pockets: 11 · best druggability 0.69

Structure

x-ray diffraction · 4 distinct chains · 31% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Apolipoprotein L1	protein	94	82% helix, 0% strand	O14791
B, H	Fab 3B6 heavy chain	protein	220	10% helix, 51% strand	—
C	Apolipoprotein L1	protein	100	81% helix, 0% strand	O14791
D, L	Fab 3B6 light chain	protein	212	8% helix, 52% strand	—

Ligands and binding sites

CL · Chloride ion · ion · 2 copies · chains B, D, L
GOL · Glycerol · additive · 2 copies · chains B, H, L

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

Pockets

11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	993	0.69	0.74	108	GOL
2	545	0.59	0.73	59	empty
3	149	0.45	0.76	35	CL
4	124	0.44	0.76	19	empty
5	102	0.43	0.78	27	empty

Interfaces

7 interfaces between chains.

H–L · 1832 Å² buried · 13 hydrogen bonds · protein-protein
B–D · 1769 Å² buried · 12 hydrogen bonds · protein-protein
C–H · 378 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 362 Å² buried · 6 hydrogen bonds · protein-protein
A–D · 361 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

7LFA · Fab 3B6 bound to ApoL1 NTD · 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 0.74

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 7LFA · PDBe 7LFA · UniProt O14791

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