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Crystal structure of glycylpeptide N-tetradecanoyltransferase from plasmodium vivax in complex with inhibitor 303A

Analyse Crystal structure of glycylpeptide N-tetradecanoyltransferase from plasmodium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6NXG
Type: protein
Length: 1,148 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: MYA, L7Y, OXM, MG, CL
Pockets: 10 · best druggability 0.83

Structure

x-ray diffraction · 2 distinct chains · 28% helix, 30% 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	378	28% helix, 30% strand	A5K1A2

Ligands and binding sites

MYA · Tetradecanoyl-coa · ligand · 3 copies · chains A, B, C
L7Y · 5-(4-chlorophenyl)-3-({[3-(morpholine-4-carbonyl) phenyl]amino}methyl)pyridin-2(1H)-one · ligand · 2 copies · chains A, B
OXM · Oxamic acid · ligand · chains A
MG · Magnesium ion · metal · 3 copies · chains A, B, C
CL · Chloride ion · ion · 3 copies · chains A, B, C
BME · Beta-mercaptoethanol · additive · 3 copies · chains A, B, C
EDO · 1,2-ethanediol · additive · chains B

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

Pockets

10 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	809	0.83	0.86	90	empty
2	841	0.80	0.82	75	MG, L7Y, MYA, EDO
3	885	0.80	0.82	71	MYA, MG
4	878	0.79	0.81	88	MG, L7Y, MYA
5	121	0.43	0.76	16	empty

Interfaces

2 interfaces between chains.

A–B · 644 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 215 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

6NXG · Crystal structure of glycylpeptide N-tetradecanoyltransferase from Plasmodium vivax in… · the same entry in another collection · chain A against A, TM-score 1.00

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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 6NXG · PDBe 6NXG · UniProt A5K1A2

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