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Fab 7D6 bound to APOL1 ntd

Analyse Fab 7D6 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: 7LFB
Type: protein
Length: 518 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab 7D6 heavy chain; Fab 7D6 light chain; Apolipoprotein L1
UniProt: O14791
Ligands: SO4
Pockets: 5 · best druggability 0.63

Structure

x-ray diffraction · 3 distinct chains · 19% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Fab 7D6 heavy chain	protein	224	11% helix, 52% strand	—
L	Fab 7D6 light chain	protein	214	6% helix, 52% strand	—
X	Apolipoprotein L1	protein	80	75% helix, 0% strand	O14791

Ligands and binding sites

SO4 · Sulfate ion · ion · 2 copies · chains L
GOL · Glycerol · additive · 2 copies · chains H, L
MES · 2-(N-morpholino)-ethanesulfonic acid · 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	634	0.63	0.74	68	MES
2	187	0.53	0.78	28	empty
3	116	0.40	0.75	23	GOL
4	104	0.35	0.73	20	empty
5	81	0.35	0.75	15	empty

Interfaces

3 interfaces between chains.

H–L · 2096 Å² buried · 13 hydrogen bonds · protein-protein
H–X · 631 Å² buried · 15 hydrogen bonds · protein-protein
L–X · 368 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

7LFB · Fab 7D6 bound to ApoL1 NTD · the same entry in another collection · chain H against H, TM-score 1.00
O14791 · AlphaFold monomer V2.0 prediction for apolipoprotein L1 (O14791) · a predicted model of the same protein · chain X against A, TM-score 0.48

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 7LFB · PDBe 7LFB · UniProt O14791

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