MolNFT v1 · #102607 · protein

Lingo-1/LI81 Fab complex

4OQT · Leucine-rich repeat and immunoglobulin-like domain…: “Lingo-1/LI81 Fab complex”. X-ray diffraction, 2 ligands (NAG, BMA), 7 pockets (best druggability 0.55). MolNFT v1 #102607 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 4OQT
Type: protein
Length: 910 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Leucine-rich repeat and immunoglobulin-like domain- containing nogo receptor-interacting…
UniProt: Q96FE5
Ligands: NAG, BMA
Pockets: 7 · best druggability 0.55

Structure

x-ray diffraction · 3 distinct chains · 6% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Leucine-rich repeat and immunoglobulin-like domain- containing nogo receptor-interacting protein 1	protein	475	7% helix, 26% strand	Q96FE5
L	Light chain of LI81 Fab, kappa 3	protein	214	5% helix, 50% strand	—
H	Heavy chain of LI81 Fab, VH3-23	protein	221	5% helix, 51% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, L
BMA · beta-D-mannopyranose · sugar · 3 copies

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

Pockets

7 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	280	0.55	0.76	38	empty
2	320	0.51	0.73	38	empty
3	193	0.47	0.75	32	empty
4	123	0.36	0.73	23	empty
5	104	0.36	0.74	24	empty

Interfaces

3 interfaces between chains.

L–H · 1782 Å² buried · 23 hydrogen bonds · protein-protein
A–L · 495 Å² buried · 14 hydrogen bonds · protein-protein
A–H · 393 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 9 disulfide, 7 glycan (disulfide, N-glycosylation).

Compared structures

4OQT · LINGO-1/Li81 Fab complex · the same entry in another collection · chain A against A, TM-score 1.00
Q96FE5 · AlphaFold monomer V2.0 prediction for leucine-rich repeat and immunoglobulin-like… · a predicted model of the same protein · chain A against A, TM-score 0.99

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 Q96FE5
Elsewhere: RCSB PDB 4OQT · PDBe 4OQT · UniProt Q96FE5

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