3IWE

Crystal Structure of human type-I N-myristoyltransferase with bound myristoyl-CoA and inhibitor DDD85646

PDB DOI: https://doi.org/10.2210/pdb3IWE/pdb

Deposited: 2009-09-02 Released: 2009-09-15
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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.79 Å
R-Value Free:
0.219 (Depositor), 0.220 (DCC)
R-Value Work:
0.180 (Depositor), 0.180 (DCC)
R-Value Observed:
0.182 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Crystal Structure of human type-I N-myristoyltransferase with bound myristoyl-CoA and inhibitor DDD85646

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.

Macromolecule Content

Total Structure Weight: 92.03 kDa
Atom Count: 7,527
Modelled Residue Count: 763
Deposited Residue Count: 766
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P30419
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MYA Query on MYA Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B]	C [auth A], E [auth B]	TETRADECANOYL-COA C₃₅ H₆₂ N₇ O₁₇ P₃ S DUAFKXOFBZQTQE-QSGBVPJFSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
646 Query on 646 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B]	D [auth A], F [auth B]	2,6-dichloro-4-(2-piperazin-1-ylpyridin-4-yl)-N-(1,3,5-trimethyl-1H-pyrazol-4-yl)benzenesulfonamide C₂₁ H₂₄ Cl₂ N₆ O₂ S XMBSZPZJLPTFMV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
646	BindingDB: 3IWE	Ki: min: 4, max: 300 (nM) from 13 assay(s)
646	BindingDB: 3IWE	IC50: min: 3, max: 4 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.79 Å
R-Value Free: 0.219 (Depositor), 0.220 (DCC)
R-Value Work: 0.180 (Depositor), 0.180 (DCC)
R-Value Observed: 0.182 (Depositor)

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.287	α = 90
b = 77.654	β = 90
c = 179.568	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2009-09-15

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2009-09-15
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2011-10-12
Changes: Atomic model
Version 1.3: 2011-11-16
Changes: Other
Version 1.4: 2024-02-21
Changes: Data collection, Database references, Derived calculations

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3IWE

Crystal Structure of human type-I N-myristoyltransferase with bound myristoyl-CoA and inhibitor DDD85646

Crystal Structure of human type-I N-myristoyltransferase with bound myristoyl-CoA and inhibitor DDD85646

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)