MolNFT v1 · #126471 · protein

Crystal structure of nigritoxine

5M41: “Crystal structure of nigritoxine”. X-ray diffraction, 1 ligand (MG), 12 pockets (best druggability 0.71). MolNFT v1 #126471 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5M41
Type: protein
Length: 712 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nigritoxine
UniProt: F0V195
Ligands: MG
Pockets: 12 · best druggability 0.71

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Nigritoxine	protein	712	41% helix, 20% strand	F0V195

Ligands and binding sites

MG · Magnesium ion · metal · chains A

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

Pockets

12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	611	0.71	0.79	54	empty
2	173	0.60	0.83	24	empty
3	257	0.57	0.78	32	empty
4	129	0.53	0.81	25	empty
5	167	0.51	0.78	22	empty

Compared structures

5M41 · Crystal structure of nigritoxine · 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
Every structure of UniProt F0V195
Elsewhere: RCSB PDB 5M41 · PDBe 5M41 · UniProt F0V195

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