MolNFT v1 · #111223 · protein

Mnemiopsis leidyi ML032222A iglur lbd glycine complex

4YKI: “Mnemiopsis leidyi ML032222A iglur lbd glycine complex”. X-ray diffraction, 3 ligands (GLY, MG, SO4), 7 pockets (best druggability 0.55). MolNFT v1 #111223 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4YKI
Type: protein
Length: 502 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ML032222A iglur
Ligands: GLY, MG, SO4
Pockets: 7 · best druggability 0.55

Structure

x-ray diffraction · 2 distinct chains · 35% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	ML032222A iglur	protein	247	36% helix, 27% strand	—
B	ML032222A iglur	protein	255	35% helix, 25% strand	—

Ligands and binding sites

GLY · Glycine · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · chains A, B
SO4 · Sulfate ion · ion · chains B

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	190	0.55	0.79	32	empty
2	124	0.52	0.81	21	empty
3	111	0.48	0.80	19	empty
4	58	0.31	0.76	14	empty
5	54	0.30	0.76	14	empty

Interfaces

1 interface between chains.

A–B · 1069 Å² buried · 19 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

4YKI · Mnemiopsis leidyi ML032222a iGluR LBD glycine complex · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 4YKI · PDBe 4YKI

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