MolNFT v1 · #100446 · protein

Structure of lymphotoxin alpha bound to anti-lta Fab

4MXV · Lymphotoxin-alpha: “Structure of lymphotoxin alpha bound to anti-lta Fab”. X-ray diffraction, 19 pockets (best druggability 0.79). MolNFT v1 #100446 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4MXV
Type: protein
Length: 1,678 residues
Chains: 9
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lymphotoxin-alpha; Anti-lymphotoxin alpha antibody light chain; Anti-lymphotoxin alpha…
UniProt: P01374
Pockets: 19 · best druggability 0.79

Structure

x-ray diffraction · 4 distinct chains · 4% helix, 53% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Lymphotoxin-alpha	protein	137	2% helix, 54% strand	P01374
D	Lymphotoxin-alpha	protein	132	2% helix, 55% strand	P01374
E, L, X	Anti-lymphotoxin alpha antibody light chain	protein	211	4% helix, 52% strand	—
F, H, Y	Anti-lymphotoxin alpha antibody heavy chain	protein	213	7% helix, 52% strand	—

Pockets

19 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	970	0.79	0.81	65	empty
2	353	0.59	0.77	52	empty
3	409	0.56	0.74	49	empty
4	339	0.53	0.74	48	empty
5	271	0.52	0.75	38	empty

Interfaces

12 interfaces between chains.

X–Y · 1760 Å² buried · 9 hydrogen bonds · protein-protein
L–H · 1746 Å² buried · 13 hydrogen bonds · protein-protein
E–F · 1715 Å² buried · 13 hydrogen bonds · protein-protein
A–D · 912 Å² buried · 7 hydrogen bonds · protein-protein
B–D · 910 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide (disulfide).

Compared structures

4MXV · Structure of Lymphotoxin alpha bound to anti-LTa Fab · the same entry in another collection · chain Y against Y, TM-score 1.00
P01374 · AlphaFold monomer V2.0 prediction for lymphotoxin-alpha (P01374) · a predicted model of the same protein · chain D against A, TM-score 0.96

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 P01374
Elsewhere: RCSB PDB 4MXV · PDBe 4MXV · UniProt P01374

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