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Plasmodium vivax N-myristoyltransferase with a bound benzofuran inhibitor (compound 23)

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: 4B12
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: C23, NHW, MG, CL, SO4
Pockets: 8 · best druggability 0.81

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	27% helix, 30% strand	A5K1A2
C	Glycylpeptide N-tetradecanoyltransferase (EC 2.3.1.97)	protein	368	27% helix, 31% strand	A5K1A2

Ligands and binding sites

C23 · 1-[3-methyl-4-(piperidin-4-yloxy)-1-benzofuran-2-yl]-3-phenylpropan-1-one · 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
DMS · Dimethyl sulfoxide · additive · 8 copies · chains A, B, C

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	1005	0.81	0.82	96	empty
2	982	0.80	0.81	91	C23, NHW, DMS, MG
3	845	0.79	0.82	77	C23, NHW, DMS, MG
4	1125	0.79	0.80	103	C23, NHW, DMS, MG
5	112	0.40	0.75	19	empty

Interfaces

2 interfaces between chains.

A–B · 430 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 124 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

4B12 · Plasmodium vivax N-myristoyltransferase with a bound benzofuran inhibitor (compound 23) · 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 4B12 · PDBe 4B12 · UniProt A5K1A2

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