MolNFT v1 · #117388 · protein

Crystal structure of C. elegans lgg-2 bound to an AIM/LIR motif

5E6O · Protein lgg-2: “Crystal structure of C. elegans lgg-2 bound to an AIM/LIR motif”. X-ray diffraction, 8 pockets (best druggability 0.70). MolNFT v1 #117388 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5E6O
Type: protein
Length: 477 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein lgg-2; TRP-glu-glu-leu
UniProt: Q23536
Pockets: 8 · best druggability 0.70

Structure

x-ray diffraction · 4 distinct chains · 31% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein lgg-2	protein	117	32% helix, 22% strand	Q23536
B	Protein lgg-2	protein	116	32% helix, 23% strand	Q23536
C, D	Protein lgg-2	protein	114	31% helix, 23% strand	Q23536
E, F, G, H	TRP-glu-glu-leu	protein	4	0% helix, 50% strand	—

Pockets

8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	436	0.70	0.81	76	empty
2	253	0.68	0.84	44	empty
3	148	0.63	0.86	35	empty
4	145	0.50	0.79	28	empty
5	120	0.40	0.75	26	empty

Interfaces

11 interfaces between chains.

A–B · 790 Å² buried · 12 hydrogen bonds · protein-protein
C–D · 704 Å² buried · 9 hydrogen bonds · protein-protein
B–C · 555 Å² buried · 3 hydrogen bonds · protein-protein
A–D · 553 Å² buried · 5 hydrogen bonds · protein-protein
B–E · 528 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

5E6O · Crystal structure of C. elegans LGG-2 bound to an AIM/LIR motif · the same entry in another collection · chain H against H, TM-score 1.00
Q23536 · AlphaFold monomer V2.0 prediction for protein lgg-2 (Q23536) · a predicted model of the same protein · chain C against A, TM-score 0.98

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 Q23536
Elsewhere: RCSB PDB 5E6O · PDBe 5E6O · UniProt Q23536

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