8Q3D

HsNMT1 in complex with both MyrCoA and GNCFSKPR(NH2) inhibitor peptide

• PDB DOI: https://doi.org/10.2210/pdb8Q3D/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens, unidentified
• Expression System: Escherichia coli, synthetic construct
• Mutation(s): No 


• Deposited: 2023-08-04 Released: 2024-08-14 
• Deposition Author(s): Dian, C., Giglione, C., Meinnel, T.
• Funding Organization(s): Agence Nationale de la Recherche (ANR), Fondation ARC, French Infrastructure for Integrated Structural Biology (FRISBI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.187 
• R-Value Work: 0.142 
• R-Value Observed: 0.145 

Starting Model: experimental

Literature

HsNMT1 in complex with both MyrCoA and GNCFSKPR(NH2) inhibitor peptide

Dian, C., Giglione, C., Meinnel, T., Riviere, F., Dutheil, F.R., Monassa, P.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 97.1 kDa 
• Atom Count: 7,237 
• Modelled Residue Count: 801 
• Deposited Residue Count: 818 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycylpeptide N-tetradecanoyltransferase 1	A	401	Homo sapiens	Mutation(s): 0  Gene Names: NMT1 EC: 2.3.1 (UniProt), 2.3.1.97 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P30419 (Homo sapiens) Explore P30419  Go to UniProtKB:  P30419
PHAROS:  P30419 GTEx:  ENSG00000136448

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycylpeptide N-tetradecanoyltransferase 1	B	401	Homo sapiens	Mutation(s): 0  Gene Names: NMT1 EC: 2.3.1 (UniProt), 2.3.1.97 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P30419 (Homo sapiens) Explore P30419  Go to UniProtKB:  P30419
PHAROS:  P30419 GTEx:  ENSG00000136448

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
GNCFSKP(AAR)	C, D	8	unidentified	Mutation(s): 0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
COA (Subject of Investigation/LOI)	E [auth A], I [auth B]	COENZYME A C21 H36 N7 O16 P3 S RGJOEKWQDUBAIZ-IBOSZNHHSA-N
MYR (Subject of Investigation/LOI)	N [auth C], O [auth D]	MYRISTIC ACID C14 H28 O2 TUNFSRHWOTWDNC-UHFFFAOYSA-N
GOL	F [auth A], G [auth A], J [auth B], K [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	H [auth A], L [auth B], M [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
AAR	C, D	L-PEPTIDE LINKING	C6 H16 N5 O		ARG

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.187 
• R-Value Work: 0.142 
• R-Value Observed: 0.145 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.8	α = 90
b = 178.34	β = 90
c = 58.26	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-08-14 
Deposition Author(s): Dian, C., Giglione, C., Meinnel, T.

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Funding Organization	Location	Grant Number
Agence Nationale de la Recherche (ANR)	France	ANR-20-CE44-0013
Agence Nationale de la Recherche (ANR)	France	ANR-2010-BLAN-1611-01
Fondation ARC	France	ARCPJA32020060002137
French Infrastructure for Integrated Structural Biology (FRISBI)	France	ANR-10-INSB-05-01

Revision History  

• Version 1.0: 2024-08-14
  Type: Initial release