MolNFT v1 · #180926 · protein

Fab 6D12 bound to APOL1 ntd

7LF7 · Fab 6D12 heavy chain: “Fab 6D12 bound to APOL1 ntd”. X-ray diffraction, 11 pockets (best druggability 0.72). MolNFT v1 #180926 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7LF7
Type: protein
Length: 1,024 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab 6D12 heavy chain; Fab 6D12 light chain; Apolipoprotein L1
UniProt: O14791
Pockets: 11 · best druggability 0.72

Structure

x-ray diffraction · 6 distinct chains · 19% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Fab 6D12 heavy chain	protein	219	8% helix, 52% strand	—
B	Fab 6D12 light chain	protein	213	6% helix, 50% strand	—
H	Fab 6D12 heavy chain	protein	223	8% helix, 49% strand	—
K	Apolipoprotein L1	protein	77	86% helix, 0% strand	O14791
L	Fab 6D12 light chain	protein	214	6% helix, 50% strand	—
M	Apolipoprotein L1	protein	78	86% helix, 0% strand	O14791

Ligands and binding sites

GOL · Glycerol · additive · 4 copies · chains K, M
EOH · Ethanol · additive · 2 copies · chains B, 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, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	821	0.72	0.77	58	GOL
2	937	0.68	0.74	98	empty
3	270	0.62	0.80	37	empty
4	318	0.54	0.75	40	empty
5	103	0.53	0.83	20	empty

Interfaces

11 interfaces between chains.

H–L · 2008 Å² buried · 18 hydrogen bonds · protein-protein
A–B · 1978 Å² buried · 18 hydrogen bonds · protein-protein
A–M · 357 Å² buried · 3 hydrogen bonds · protein-protein
H–K · 349 Å² buried · 3 hydrogen bonds · protein-protein
B–M · 249 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide, 1 modified (disulfide, oxidation).

Compared structures

7LF7 · Fab 6D12 bound to ApoL1 NTD · the same entry in another collection · chain M against M, TM-score 1.00
O14791 · AlphaFold monomer V2.0 prediction for apolipoprotein L1 (O14791) · a predicted model of the same protein · chain K against A, TM-score 0.80

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 7LF7 · PDBe 7LF7 · UniProt O14791

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