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)

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
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

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.

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycylpeptide N-tetradecanoyltransferase 1	A	401	Homo sapiens	Mutation(s): 0 Gene Names: NMT1
UniProt & NIH Common Fund Data Resources
Find proteins for P30419 (Homo sapiens) Explore P30419 Go to UniProtKB: P30419
PHAROS: P30419 GTEx: ENSG00000136448
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P30419
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycylpeptide N-tetradecanoyltransferase 1	B	401	Homo sapiens	Mutation(s): 0 Gene Names: NMT1
UniProt & NIH Common Fund Data Resources
Find proteins for P30419 (Homo sapiens) Explore P30419 Go to UniProtKB: P30419
PHAROS: P30419 GTEx: ENSG00000136448
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P30419
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
COA (Subject of Investigation/LOI) Query on COA Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B]	E [auth A], I [auth B]	COENZYME A C₂₁ H₃₆ N₇ O₁₆ P₃ S RGJOEKWQDUBAIZ-IBOSZNHHSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B]
MYR (Subject of Investigation/LOI) Query on MYR Download Ideal Coordinates CCD File SDF format, chain N [auth C] SDF format, chain O [auth D] MOL2 format, chain N [auth C] MOL2 format, chain O [auth D]	N [auth C], O [auth D]	MYRISTIC ACID C₁₄ H₂₈ O₂ TUNFSRHWOTWDNC-UHFFFAOYSA-N		Interactions Focus chain N [auth C] Focus chain O [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain F [auth A]	F [auth A], G [auth A], J [auth B], K [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B]	H [auth A], L [auth B], M [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
AAR Query on 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

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-08-14

Deposition Author(s):

Dian, C.

Giglione, C.

Meinnel, T.

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