[English] 日本語
Yorodumi
- PDB-5v0w: Crystal structure of glycylpeptide N-tetradecanoyltransferase fro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5v0w
TitleCrystal structure of glycylpeptide N-tetradecanoyltransferase from Plasmodium vivax in complex with inhibitor IMP-0001088
ComponentsGlycylpeptide N-tetradecanoyltransferase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / SSGCID / glycylpeptide N-tetradecanoyltransferase / N-myristoyltransferase / NMT / Plasmodium vival / Salvador I / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


glycylpeptide N-tetradecanoyltransferase / glycylpeptide N-tetradecanoyltransferase activity / metal ion binding / 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-KFK / TETRADECANOYL-COA / Glycylpeptide N-tetradecanoyltransferase / Glycylpeptide N-tetradecanoyltransferase
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2025
Title: Structure of Plasmodium vivax N-myristoyltransferase with inhibitor IMP-1088: exploring an NMT inhibitor for antimalarial therapy
Authors: Mendez, A. / Bolling, C. / Taylor, S. / Makumire, S. / Staker, B. / Reers, A. / Hammerson, B. / Mayclin, S.J. / Abendroth, J. / Lorimer, D.D. / Edwards, T.E. / Tate, E.W. / Subramanian, S. / ...Authors: Mendez, A. / Bolling, C. / Taylor, S. / Makumire, S. / Staker, B. / Reers, A. / Hammerson, B. / Mayclin, S.J. / Abendroth, J. / Lorimer, D.D. / Edwards, T.E. / Tate, E.W. / Subramanian, S. / Bell, A.S. / Myler, P.J. / Asojo, O.A. / Chakafana, G.
History
DepositionFeb 28, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 15, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)147,28125
Polymers141,7533
Non-polymers5,52822
Water30,1931676
1
A: Glycylpeptide N-tetradecanoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1028
Polymers47,2511
Non-polymers1,8517
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycylpeptide N-tetradecanoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1389
Polymers47,2511
Non-polymers1,8878
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Glycylpeptide N-tetradecanoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0418
Polymers47,2511
Non-polymers1,7917
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.320, 119.130, 176.610
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
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 / Production host: Eschericia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A0A1G4HIY1, UniProt: A5K1A2*PLUS, glycylpeptide N-tetradecanoyltransferase

-
Non-polymers , 5 types, 1698 molecules

#2: Chemical ChemComp-MYA / TETRADECANOYL-COA / MYRISTOYL-COA


Mass: 977.890 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C35H62N7O17P3S
#3: Chemical ChemComp-KFK / 1-[5-[3,4-bis(fluoranyl)-2-[2-(1,3,5-trimethylpyrazol-4-yl)ethoxy]phenyl]-1-methyl-indazol-3-yl]-~{N},~{N}-dimethyl-methanamine


Mass: 453.527 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C25H29F2N5O / Comment: inhibitor*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1676 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.17 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 27% PEG 3350, 200 mM Ammonium Sulfate, 100 mM BisTris pH 6.0, 0.5mM IMP-0001088, 0.5mM myristoyl CoA; protein conc 12.53mg/mL; hdg0-9

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jan 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 112736 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.248 % / Biso Wilson estimate: 12.32 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.107 / Rrim(I) all: 0.115 / Χ2: 1.04 / Net I/σ(I): 15.21
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.8-1.856.2680.5153.7482130.9050.56299.4
1.85-1.97.3420.4285.0380030.9410.461100
1.9-1.957.3950.375.8478450.9560.398100
1.95-2.017.390.2917.2776020.970.313100
2.01-2.087.3730.2468.673340.9750.265100
2.08-2.157.3690.2061071690.9830.222100
2.15-2.237.3750.17811.4969070.9870.192100
2.23-2.327.3360.1541366500.9890.166100
2.32-2.437.3640.13814.1663780.9910.149100
2.43-2.557.3580.12715.0961100.9930.13799.9
2.55-2.687.3540.11516.7658080.9930.124100
2.68-2.857.3390.09819.1355460.9950.105100
2.85-3.047.3330.08621.1851960.9960.092100
3.04-3.297.2730.06925.2548270.9970.07499.9
3.29-3.67.2480.05928.8945100.9980.06499.9
3.6-4.027.2550.05132.0840860.9980.054100
4.02-4.657.2210.04435.1536010.9990.04799.9
4.65-5.697.2470.04334.3630990.9990.047100
5.69-8.057.1310.04631.2324370.9990.05100
8.05-506.6110.03637.6714150.9990.03999.4

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
Cootmodel building
PHENIXrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4b14

4b14


Resolution: 1.8→49.575 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.16
RfactorNum. reflection% reflection
Rfree0.184 2031 1.8 %
Rwork0.1466 --
obs0.1473 112717 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 90.87 Å2 / Biso mean: 16.217 Å2 / Biso min: 0.91 Å2
Refinement stepCycle: final / Resolution: 1.8→49.575 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9405 0 348 1697 11450
Biso mean--16.28 27.54 -
Num. residues----1147
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00710204
X-RAY DIFFRACTIONf_angle_d0.93513929
X-RAY DIFFRACTIONf_chiral_restr0.0611497
X-RAY DIFFRACTIONf_plane_restr0.0061721
X-RAY DIFFRACTIONf_dihedral_angle_d15.5126079
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7999-1.84180.29181190.22687250736999
1.8418-1.88790.20991370.18872837420100
1.8879-1.93890.1921150.164272987413100
1.9389-1.9960.19431360.15272987434100
1.996-2.06040.19241250.146973537478100
2.0604-2.1340.17721460.144273067452100
2.134-2.21950.2221260.147173367462100
2.2195-2.32050.2011550.145673177472100
2.3205-2.44280.20121330.146673347467100
2.4428-2.59590.18091210.155573997520100
2.5959-2.79630.20011270.154973517478100
2.7963-3.07760.2121540.151373997553100
3.0776-3.52290.15861490.132374317580100
3.5229-4.4380.13691190.116775657684100
4.438-49.59410.16461690.142977667935100
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)
10.5550.0275-0.00560.6820.17990.4721-0.00130.01490.0390.0070.0305-0.06850.00250.0326-0.0260.073-0.0075-0.00590.08480.00370.071338.2447-21.9053-15.0752
20.8349-0.17410.12080.3365-0.03020.35210.0060.06180.066-0.00960.0010.0083-0.0267-0.0247-0.00550.0659-0.00480.0050.06730.00520.06514.8843-23.9799-22.3693
32.53770.05751.27411.72330.71723.1448-0.037-0.18480.22840.1617-0.1228-0.0143-0.197-0.14150.13830.07410.01060.01890.1121-0.02580.1009-5.0773-42.1739-39.7447
42.64330.9357-0.51380.8019-0.34921.0163-0.03920.3020.0356-0.07570.05540.0526-0.0093-0.0266-0.0010.09570.0139-0.00950.1154-0.00210.06335.021-46.2607-64.6034
51.04670.4022-0.21030.4473-0.07250.37690.0170.09950.054-0.0248-0.01010.0118-0.0175-0.045-0.00250.07730.0159-0.00090.08920.00180.07126.8337-43.0034-54.7994
61.0271-0.04310.13551.5889-0.69110.7734-0.00130.06130.0190.1354-0.0705-0.1946-0.08040.07230.07240.08260.01330.0160.11250.00610.085737.6749-38.9438-53.5891
72.1609-0.3986-0.30482.47780.66972.9058-0.0476-0.0179-0.22530.0907-0.0152-0.02920.21680.01250.0550.0461-0.0017-0.00560.08070.00980.081921.287-54.6644-46.4131
81.38750.3288-0.39130.40340.00690.65630.0210.01140.0549-0.0148-0.0049-0.0476-0.01560.0441-0.01560.0639-0.0017-0.00250.06880.00630.064523.3963-40.8959-50.0502
91.7344-0.92460.07882.8422-0.47041.2375-0.0769-0.05470.21240.0720.0433-0.1543-0.18020.01030.02460.068-0.0231-0.01860.0583-0.0060.119224.0876-58.8806-12.5618
101.4980.0569-0.54180.797-0.15080.9405-0.0414-0.0568-0.1370.02990.008-0.00920.07860.00680.02230.0755-0.0063-0.00940.06970.00180.074913.1727-82.3726-4.8767
110.7373-0.1271-0.18890.56240.12310.48140.0086-0.0228-0.0108-0.0213-0.0066-0.02960.01-0.00430.00970.0542-0.0117-0.00450.06710.00780.063815.4192-72.7704-9.8961
121.076-0.21260.02280.55070.16280.7541-0.1177-0.22070.07250.11720.0350.07540.0004-0.01370.04510.09720.0034-0.00160.15030.00250.125-15.827-70.4834-1.1677
132.9652.77380.51125.86931.24881.6143-0.11340.22120.0002-0.32620.041-0.015-0.096-0.0161-0.00560.07490.0016-0.01070.14090.01430.0882-6.175-66.987-24.0666
141.3720.36110.12951.80570.11331.0807-0.06260.1641-0.0659-0.14780.1219-0.01610.0629-0.0782-0.01540.0541-0.00070.00110.10410.0080.0608-0.5775-72.1799-18.9744
151.1407-0.00030.08431.0018-0.29871.57380.0107-0.0973-0.12440.01330.05840.05430.029-0.1322-0.03850.04150.00320.02170.06940.00660.0684-8.3938-74.2933-6.6752
161.31590.3032-0.08380.4511-0.03510.29790.04-0.08170.06710.0072-0.02910.0496-0.0241-0.0431-0.0060.07460.0055-0.00290.0825-0.00360.0829-3.5355-63.2202-7.3505
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 26 through 198 )A26 - 198
2X-RAY DIFFRACTION2chain 'A' and (resid 199 through 410 )A199 - 410
3X-RAY DIFFRACTION3chain 'B' and (resid 26 through 59 )B26 - 59
4X-RAY DIFFRACTION4chain 'B' and (resid 60 through 116 )B60 - 116
5X-RAY DIFFRACTION5chain 'B' and (resid 117 through 234 )B117 - 234
6X-RAY DIFFRACTION6chain 'B' and (resid 235 through 257 )B235 - 257
7X-RAY DIFFRACTION7chain 'B' and (resid 258 through 296 )B258 - 296
8X-RAY DIFFRACTION8chain 'B' and (resid 297 through 410 )B297 - 410
9X-RAY DIFFRACTION9chain 'C' and (resid 25 through 59 )C25 - 59
10X-RAY DIFFRACTION10chain 'C' and (resid 60 through 116 )C60 - 116
11X-RAY DIFFRACTION11chain 'C' and (resid 117 through 215 )C117 - 215
12X-RAY DIFFRACTION12chain 'C' and (resid 216 through 257 )C216 - 257
13X-RAY DIFFRACTION13chain 'C' and (resid 258 through 274 )C258 - 274
14X-RAY DIFFRACTION14chain 'C' and (resid 275 through 296 )C275 - 296
15X-RAY DIFFRACTION15chain 'C' and (resid 297 through 331 )C297 - 331
16X-RAY DIFFRACTION16chain 'C' and (resid 332 through 410 )C332 - 410

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more