MolNFT v1 · #128896 · protein

P.VIVAX nmt with an aminomethylindazole inhibitor bound

5O48 · Glycylpeptide N-tetradecanoyltransferase: “P.VIVAX nmt with an aminomethylindazole inhibitor bound”. X-ray diffraction, 5 ligands (NHW, 9K2, MG), 8 pockets (best druggability 0.80). MolNFT v1 #128896 on GenesisL1: 3D structure…

PDB: 5O48
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: NHW, 9K2, MG, SO4, CL
Pockets: 8 · best druggability 0.80

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

NHW · 2-oxopentadecyl-CoA · ligand · 3 copies · chains A, B, C
9K2 · 1-[5-(4-fluoranyl-2-methyl-phenyl)-1~{H}-indazol-3-yl]-~{N},~{N}-dimethyl-methanamine · ligand · 3 copies · chains A, B, C
MG · Magnesium ion · metal · 3 copies · chains A, B, C
SO4 · Sulfate ion · ion · 4 copies · chains A, B, C
CL · Chloride ion · ion · 3 copies · chains A, B, C
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	944	0.80	0.82	93	NHW, 9K2, DMS, MG
2	982	0.80	0.81	90	NHW, 9K2, DMS, MG
3	896	0.79	0.81	85	NHW, 9K2, DMS, MG
4	1179	0.79	0.81	101	empty
5	136	0.42	0.75	16	empty

Interfaces

2 interfaces between chains.

A–B · 457 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 119 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

5O48 · P.vivax NMT with an aminomethylindazole inhibitor bound · 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 5O48 · PDBe 5O48 · UniProt A5K1A2

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