3JTK

Crystal Structure of human type-I N-myristoyltransferase with bound myristoyl-CoA and inhibitor DDD90055

• PDB DOI: https://doi.org/10.2210/pdb3JTK/pdb

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


• Deposited: 2009-09-12 Released: 2009-09-22 
• Deposition Author(s): Qiu, W., Hutchinson, A., Wernimont, A., Lin, Y.-H., Kania, A., Ravichandran, M., Kozieradzki, I., Cossar, D., Schapira, M., Arrowsmith, C.H., Bountra, C., Weigelt, J., Edwards, A.M., Wyatt, P.G., Ferguson, M.A.J., Frearson, J.A., Brand, S.Y., Robinson, D.A., Bochkarev, A., Hui, R., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free: 0.221 
• R-Value Work: 0.198 
• R-Value Observed: 0.199 

Starting Model: experimental

Literature

Crystal Structure of human type-I N-myristoyltransferase with bound myristoyl-CoA and inhibitor DDD90055

Qiu, W., Hutchinson, A., Wernimont, A., Lin, Y.-H., Kania, A., Ravichandran, M., Kozieradzki, I., Cossar, D., Schapira, M., Arrowsmith, C.H., Bountra, C., Weigelt, J., Edwards, A.M., Wyatt, P.G., Ferguson, M.A.J., Frearson, J.A., Brand, S.Y., Robinson, D.A., Bochkarev, A., Hui, R.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 91.43 kDa 
• Atom Count: 7,285 
• Modelled Residue Count: 760 
• Deposited Residue Count: 766 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycylpeptide N-tetradecanoyltransferase 1	A, B	383	Homo sapiens	Mutation(s): 0  Gene Names: NMT, NMT1 EC: 2.3.1.97 (PDB Primary Data), 2.3.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P30419 (Homo sapiens) Explore P30419  Go to UniProtKB:  P30419
PHAROS:  P30419 GTEx:  ENSG00000136448

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MYA	C [auth A], E [auth B]	TETRADECANOYL-COA C35 H62 N7 O17 P3 S DUAFKXOFBZQTQE-QSGBVPJFSA-N
X55	D [auth A]	(2R)-3-benzyl-2-(2-bromo-4-hydroxy-5-methoxyphenyl)-1,3-thiazolidin-4-one C17 H16 Br N O3 S IHRIZEYEEMHXFS-QGZVFWFLSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free: 0.221 
• R-Value Work: 0.198 
• R-Value Observed: 0.199 
• Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.247	α = 90
b = 79.023	β = 90
c = 178.381	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-22 
Deposition Author(s): Qiu, W., Hutchinson, A., Wernimont, A., Lin, Y.-H., Kania, A., Ravichandran, M., Kozieradzki, I., Cossar, D., Schapira, M., Arrowsmith, C.H., Bountra, C., Weigelt, J., Edwards, A.M., Wyatt, P.G., Ferguson, M.A.J., Frearson, J.A., Brand, S.Y., Robinson, D.A., Bochkarev, A., Hui, R., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2009-09-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-11-16
  Changes: Other
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description