Research workbench

Human neurofibromin 2/MERLIN/SCHWANNOMIN residues 1-339 in complex with PIP2

Analyse Human neurofibromin 2/MERLIN/SCHWANNOMIN residues 1-339 in complex with PIP2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6CDS
Type: protein
Length: 650 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Merlin
UniProt: P35240
Ligands: PIO, PO4
Pockets: 12 · best druggability 0.60

Structure

x-ray diffraction · 1 distinct chain · 42% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Merlin	protein	325	42% helix, 22% strand	P35240

Ligands and binding sites

PIO · [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2, 3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate · ligand · 2 copies · chains A, B
PO4 · Phosphate ion · ion · 2 copies · chains A, B
PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
GOL · Glycerol · additive · chains B

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

Pockets

12 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	295	0.60	0.78	29	GOL
2	253	0.57	0.78	26	empty
3	85	0.44	0.80	26	empty
4	58	0.41	0.81	15	empty
5	119	0.41	0.75	20	empty

Interfaces

1 interface between chains.

A–B · 443 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

6CDS · Human neurofibromin 2/merlin/schwannomin residues 1-339 in complex with PIP2 · the same entry in another collection · chain A against A, TM-score 1.00
P35240 · AlphaFold monomer V2.0 prediction for merlin (P35240) · a predicted model of the same protein · chain A against A, TM-score 0.91

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 P35240
Elsewhere: RCSB PDB 6CDS · PDBe 6CDS · UniProt P35240

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