Research workbench

Plasmodium vivax N-myristoyltransferase with a bound benzofuran inhibitor (compound 25)

Analyse Plasmodium vivax N-myristoyltransferase with a bound benzofuran inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4B13
Type: protein
Length: 1,138 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glycylpeptide N-tetradecanoyltransferase
EC: 2.3.1.97
UniProt: A5K1A2
Ligands: X25, NHW, MG, CL, SO4
Pockets: 8 · best druggability 0.82

Structure

x-ray diffraction · 2 distinct chains · 27% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Glycylpeptide N-tetradecanoyltransferase (EC 2.3.1.97)	protein	385	28% helix, 31% strand	A5K1A2
C	Glycylpeptide N-tetradecanoyltransferase (EC 2.3.1.97)	protein	368	27% helix, 32% strand	A5K1A2

Ligands and binding sites

X25 · 4-{[2-(3-benzyl-1,2,4-oxadiazol-5-yl)-3-methyl-1-benzofuran-4-yl]oxy}piperidine · ligand · 3 copies · chains A, B, C
NHW · 2-oxopentadecyl-CoA · ligand · 3 copies · chains A, B, C
MG · Magnesium ion · metal · 3 copies · chains A, B, C
CL · Chloride ion · ion · 3 copies · chains A, B, C
SO4 · Sulfate ion · ion · chains A, B

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

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	1078	0.82	0.83	105	empty
2	956	0.79	0.81	88	X25, NHW, MG
3	951	0.79	0.81	90	X25, NHW, MG
4	898	0.79	0.81	74	X25, NHW, MG
5	59	0.42	0.82	18	empty

Interfaces

2 interfaces between chains.

A–B · 503 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 224 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

4B13 · Plasmodium vivax N-myristoyltransferase with a bound benzofuran inhibitor (compound 25) · 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 A5K1A2
Elsewhere: RCSB PDB 4B13 · PDBe 4B13 · UniProt A5K1A2

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.