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- PDB-6mb1: Crystal structure of N-myristoyl transferase (NMT) from Plasmodiu... -

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Basic information

Entry
Database: PDB / ID: 6mb1
TitleCrystal structure of N-myristoyl transferase (NMT) from Plasmodium vivax in complex with inhibitor IMP-1002
ComponentsGlycylpeptide N-tetradecanoyltransferase
KeywordsTRANSFERASE / SSGCID / glycylpeptide N-tetradecanoyltransferase / N-myristoyltransferase / NMT / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


glycylpeptide N-tetradecanoyltransferase / glycylpeptide N-tetradecanoyltransferase activity / cytoplasm
Similarity search - Function
Aminopeptidase - #170 / Glycylpeptide N-tetradecanoyltransferase, conserved site / Myristoyl-CoA:protein N-myristoyltransferase signature 1. / Myristoyl-CoA:protein N-myristoyltransferase signature 2. / Glycylpeptide N-tetradecanoyltransferase / Glycylpeptide N-tetradecanoyltransferase, N-terminal / Glycylpeptide N-tetradecanoyltransferase, C-terminal / Myristoyl-CoA:protein N-myristoyltransferase, N-terminal domain / Myristoyl-CoA:protein N-myristoyltransferase, C-terminal domain / Acyl-CoA N-acyltransferase ...Aminopeptidase - #170 / Glycylpeptide N-tetradecanoyltransferase, conserved site / Myristoyl-CoA:protein N-myristoyltransferase signature 1. / Myristoyl-CoA:protein N-myristoyltransferase signature 2. / Glycylpeptide N-tetradecanoyltransferase / Glycylpeptide N-tetradecanoyltransferase, N-terminal / Glycylpeptide N-tetradecanoyltransferase, C-terminal / Myristoyl-CoA:protein N-myristoyltransferase, N-terminal domain / Myristoyl-CoA:protein N-myristoyltransferase, C-terminal domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-JCY / TETRADEC-13-YNOIC ACID - COA THIOESTER / Glycylpeptide N-tetradecanoyltransferase
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.5 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Cell Chem Biol / Year: 2019
Title: Structure-Guided Identification of Resistance Breaking Antimalarial N‐Myristoyltransferase Inhibitors.
Authors: Schlott, A.C. / Mayclin, S. / Reers, A.R. / Coburn-Flynn, O. / Bell, A.S. / Green, J. / Knuepfer, E. / Charter, D. / Bonnert, R. / Campo, B. / Burrows, J. / Lyons-Abbott, S. / Staker, B.L. / ...Authors: Schlott, A.C. / Mayclin, S. / Reers, A.R. / Coburn-Flynn, O. / Bell, A.S. / Green, J. / Knuepfer, E. / Charter, D. / Bonnert, R. / Campo, B. / Burrows, J. / Lyons-Abbott, S. / Staker, B.L. / Chung, C.W. / Myler, P.J. / Fidock, D.A. / Tate, E.W. / Holder, A.A.
History
DepositionAug 29, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 22, 2025Group: Structure summary / Category: audit_author / pdbx_entry_details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycylpeptide N-tetradecanoyltransferase
B: Glycylpeptide N-tetradecanoyltransferase
C: Glycylpeptide N-tetradecanoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,68021
Polymers141,7533
Non-polymers4,92718
Water32,3551796
1
A: Glycylpeptide N-tetradecanoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9167
Polymers47,2511
Non-polymers1,6656
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glycylpeptide N-tetradecanoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8827
Polymers47,2511
Non-polymers1,6316
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Glycylpeptide N-tetradecanoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8827
Polymers47,2511
Non-polymers1,6316
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.560, 119.110, 176.080
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Glycylpeptide N-tetradecanoyltransferase


Mass: 47250.945 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax)
Gene: PVC01_130042700, PVP01_1336100 / Plasmid: PlviB.18219.a.FR2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A0A1G4HIY1, glycylpeptide N-tetradecanoyltransferase

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Non-polymers , 6 types, 1814 molecules

#2: Chemical ChemComp-YNC / TETRADEC-13-YNOIC ACID - COA THIOESTER


Mass: 973.858 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C35H58N7O17P3S
#3: Chemical ChemComp-JCY / 1-(5-{4-fluoro-2-[2-(1,3,5-trimethyl-1H-pyrazol-4-yl)ethoxy]phenyl}-1-methyl-1H-indazol-3-yl)-N,N-dimethylmethanamine


Mass: 435.537 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C25H30FN5O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1796 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: 24.36% PEG 3350, 200 mM Ammonium Sulfate, 100 mM BisTris pH 6.6, 0.5mM IMP-1002, 0.5mM myristoyl CoA: PlviB.18219.a.FR2.PS38393 conc 7.8mg/mL: puck id qxk8-4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 7, 2018
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 193711 / % possible obs: 99.9 % / Redundancy: 5.783 % / Biso Wilson estimate: 19.554 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.09 / Rrim(I) all: 0.099 / Χ2: 1.051 / Net I/σ(I): 11.91
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.5-1.544.5050.4622.62142010.8040.52399.9
1.54-1.585.7090.3933.58138490.8890.433100
1.58-1.636.1380.3364.43134480.9320.368100
1.63-1.686.1440.2825.31131310.9490.308100
1.68-1.736.1330.2386.45126660.9610.26100
1.73-1.796.1450.2067.56123070.9720.225100
1.79-1.866.1010.1689.44118990.980.184100
1.86-1.945.9260.1510.99114020.9820.165100
1.94-2.025.9580.12812.75109770.9860.14100
2.02-2.125.7880.11314.46105120.9890.12499.9
2.12-2.245.7930.116.1299930.9910.10999.9
2.24-2.375.5910.09417.294720.9910.10499.9
2.37-2.545.6540.08718.1989230.9920.09699.9
2.54-2.745.6290.08119.0483020.9930.08999.8
2.74-35.6260.07420.4176830.9930.08199.8
3-3.355.5720.06721.9869680.9950.07399.7
3.35-3.875.6820.06223.3761810.9950.06899.5
3.87-4.745.8590.05424.6252690.9960.0699.6
4.74-6.715.9830.04524.2841250.9980.04999.8
6.71-505.6180.03224.0624030.9990.03699.4

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.14_3211refinement
PDB_EXTRACT3.24data extraction
PHENIXphasing
RefinementResolution: 1.5→50 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 16.37
RfactorNum. reflection% reflection
Rfree0.1826 2060 1.06 %
Rwork0.1543 --
obs0.1546 193697 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 64.41 Å2 / Biso mean: 17.0926 Å2 / Biso min: 5.44 Å2
Refinement stepCycle: final / Resolution: 1.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9412 0 325 1829 11566
Biso mean--14.28 29.04 -
Num. residues----1144
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.5-1.53490.24011350.20751262712762
1.5349-1.57320.20741420.1831267112813
1.5732-1.61580.20241170.17141266812785
1.6158-1.66330.1961450.17021263312778
1.6633-1.7170.19561290.16591270112830
1.717-1.77840.19211610.16391270812869
1.7784-1.84960.18911350.15811269512830
1.8496-1.93380.20171260.16381273312859
1.9338-2.03570.20341370.16221272212859
2.0357-2.16330.18471280.15431276812896
2.1633-2.33030.21271380.15751274912887
2.3303-2.56480.18811430.16081279412937
2.5648-2.93590.18871280.15711288513013
2.9359-3.69870.14771540.13761291113065
3.6987-48.2020.1581420.13331337213514
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9558-0.00650.16341.0238-0.25731.0834-0.0105-0.0451-0.0525-0.01850.0233-0.03910.0514-0.0238-0.01380.05810.00430.01040.0558-0.00580.063517.5544-75.3867-11.6162
22.35280.8837-0.41671.0207-0.33620.7213-0.0041-0.2090.0670.10740.02780.0994-0.0047-0.0698-0.0160.14880.0250.00220.1338-0.0130.1172-3.1698-65.4263.567
32.540.0527-0.39520.36150.1020.2171-0.0310.1525-0.0141-0.0310.0110.02950.0091-0.03210.02260.0972-0.0018-0.01320.0930.00870.0618-7.3184-70.4033-19.1678
41.34130.1482-0.2280.51640.00840.3308-0.0112-0.11140.01420.03010.00310.04960.0116-0.02880.00410.09040.01130.00370.08240.00210.0713-4.8143-66.6906-7.1598
52.39681.62940.90212.25841.77161.5116-0.09240.26670.0394-0.28220.20440.03220.03270.1183-0.10870.09410.01060.02320.1442-0.02060.113345.1077-33.7232-25.8137
60.4173-0.06630.03440.3680.01080.17680.00590.02620.0625-0.01930.0067-0.0125-0.03670.008-0.01380.0791-0.00530.00480.06470.00250.07132.2195-17.889-16.8549
71.7063-0.2397-0.08830.44030.05780.7192-0.032-0.06020.02470.04350.02360.0457-0.0077-0.04050.01040.0747-0.01320.00730.04770.00690.073412.7704-30.7275-14.3019
81.153-0.1215-0.08710.31110.01610.4370.01090.04620.0813-0.0159-0.00710.0298-0.018-0.03920.00320.0657-0.0034-0.00490.05460.00060.06216.1186-24.3287-22.8165
92.2609-0.00821.98970.23960.65313.5324-0.1143-0.10550.26840.1677-0.14810.0127-0.3072-0.110.22530.09690.00840.02010.1167-0.02470.1255-5.4348-42.4206-39.9889
102.4610.9154-0.70750.6395-0.49011.1772-0.05540.4425-0.1251-0.06620.0506-0.01160.0074-0.07750.01940.10980.0073-0.00720.1696-0.02650.0989-0.2166-50.4971-66.0484
113.15490.3831-0.3511.0601-0.27172.0551-0.0250.12760.2276-0.03840.0128-0.1147-0.20010.0863-0.01640.0823-0.0142-0.01330.11360.00180.053713.3388-40.6051-62.5808
121.29250.00270.37030.56520.18361.00140.01450.2234-0.078-0.079-0.0020.009-0.0340.0082-0.00140.0819-0.00760.01050.1196-0.01550.09222.838-51.9752-59.3394
130.95560.2699-0.11810.32960.0540.25710.0160.08660.1216-0.0241-00.0095-0.0742-0.0015-0.01060.08940.00250.00480.07780.00970.077710.494-38.2746-53.5027
141.83250.1078-0.42630.6340.14580.612-0.00910.0538-0.0986-0.0107-0.0111-0.03170.02480.00630.02970.06370.009-0.00720.07510.00150.056926.5627-51.6018-47.6601
151.24490.1885-0.33610.32270.07870.33760.01020.05510.0813-0.0250.0271-0.0305-0.03120.0251-0.03320.0702-0.00990.00010.0726-0.00020.062623.4723-40.9454-49.7114
161.9045-2.13190.4033.8709-0.86190.2766-0.1056-0.04670.18750.1560.0783-0.1909-0.2253-0.03080.02570.0875-0.0319-0.00940.088300.154624.0804-58.9201-12.9327
172.25390.0721-0.52350.7971-0.29390.8379-0.0567-0.1172-0.1340.05620.0255-0.01060.0071-0.02140.02590.09420.0084-0.00750.05770.00120.069813.4171-82.4441-4.8856
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'C' and (resid 117 through 198 )C117 - 198
2X-RAY DIFFRACTION2chain 'C' and (resid 199 through 244 )C199 - 244
3X-RAY DIFFRACTION3chain 'C' and (resid 245 through 296 )C245 - 296
4X-RAY DIFFRACTION4chain 'C' and (resid 297 through 410 )C297 - 410
5X-RAY DIFFRACTION5chain 'A' and (resid 26 through 59 )A26 - 59
6X-RAY DIFFRACTION6chain 'A' and (resid 60 through 241 )A60 - 241
7X-RAY DIFFRACTION7chain 'A' and (resid 242 through 296 )A242 - 296
8X-RAY DIFFRACTION8chain 'A' and (resid 297 through 410 )A297 - 410
9X-RAY DIFFRACTION9chain 'B' and (resid 26 through 59 )B26 - 59
10X-RAY DIFFRACTION10chain 'B' and (resid 60 through 94 )B60 - 94
11X-RAY DIFFRACTION11chain 'B' and (resid 95 through 116 )B95 - 116
12X-RAY DIFFRACTION12chain 'B' and (resid 117 through 150 )B117 - 150
13X-RAY DIFFRACTION13chain 'B' and (resid 151 through 241 )B151 - 241
14X-RAY DIFFRACTION14chain 'B' and (resid 242 through 296 )B242 - 296
15X-RAY DIFFRACTION15chain 'B' and (resid 297 through 410 )B297 - 410
16X-RAY DIFFRACTION16chain 'C' and (resid 26 through 59 )C26 - 59
17X-RAY DIFFRACTION17chain 'C' and (resid 60 through 116 )C60 - 116

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