MolNFT v1 · #111230 · protein

Mnemiopsis leidyi ML032222A iglur lbd serine complex

4YKP: “Mnemiopsis leidyi ML032222A iglur lbd serine complex”. X-ray diffraction, 1 ligand (MG), 6 pockets (best druggability 0.57). MolNFT v1 #111230 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4YKP
Type: protein
Length: 506 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ML032222A iglur
Ligands: MG
Pockets: 6 · best druggability 0.57

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	ML032222A iglur	protein	249	36% helix, 27% strand	—
B	ML032222A iglur	protein	257	35% helix, 25% strand	—

Ligands and binding sites

MG · Magnesium ion · metal · chains A, B

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

Pockets

6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	201	0.57	0.80	29	empty
2	131	0.53	0.81	21	empty
3	121	0.50	0.80	19	empty
4	68	0.32	0.75	15	empty
5	66	0.31	0.75	15	empty

Interfaces

1 interface between chains.

A–B · 1044 Å² buried · 18 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

4YKP · Mnemiopsis leidyi ML032222a iGluR LBD serine 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 4YKP · PDBe 4YKP

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