[English] 日本語
Yorodumi
- PDB-5oip: InhA (T2A mutant) complexed with 1-(Pyridin-3-ylmethyl)-3-(1-(pyr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5oip
TitleInhA (T2A mutant) complexed with 1-(Pyridin-3-ylmethyl)-3-(1-(pyrimidin-2-yl)piperidin-4-yl)urea
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsOXIDOREDUCTASE / Inhibitor / complex / fragment based drug discovery / tuberculosis
Function / homology
Function and homology information


trans-2-enoyl-CoA reductase (NADH) activity / mycolic acid biosynthetic process / fatty acid elongation / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / NAD+ binding / peptidoglycan-based cell wall / fatty acid binding / response to antibiotic / plasma membrane
Similarity search - Function
: / Enoyl-[acyl-carrier-protein] reductase (NADH) / Enoyl-(Acyl carrier protein) reductase / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-9WE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / PHOSPHATE ION / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.71 Å
AuthorsConvery, M.A.
CitationJournal: ChemMedChem / Year: 2018
Title: Screening of a Novel Fragment Library with Functional Complexity against Mycobacterium tuberculosis InhA.
Authors: Prati, F. / Zuccotto, F. / Fletcher, D. / Convery, M.A. / Fernandez-Menendez, R. / Bates, R. / Encinas, L. / Zeng, J. / Chung, C.W. / De Dios Anton, P. / Mendoza-Losana, A. / Mackenzie, C. / ...Authors: Prati, F. / Zuccotto, F. / Fletcher, D. / Convery, M.A. / Fernandez-Menendez, R. / Bates, R. / Encinas, L. / Zeng, J. / Chung, C.W. / De Dios Anton, P. / Mendoza-Losana, A. / Mackenzie, C. / Green, S.R. / Huggett, M. / Barros, D. / Wyatt, P.G. / Ray, P.C.
History
DepositionJul 19, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5964
Polymers28,5251
Non-polymers1,0713
Water5,477304
1
A: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules

A: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules

A: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules

A: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,38216
Polymers114,0994
Non-polymers4,28312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
crystal symmetry operation7_553y,x,-z-4/31
crystal symmetry operation10_663-y+1,-x+1,-z-4/31
Buried area20130 Å2
ΔGint-173 kcal/mol
Surface area34790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.140, 99.140, 141.520
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-456-

HOH

21A-497-

HOH

-
Components

#1: Protein Enoyl-[acyl-carrier-protein] reductase [NADH] / Enoyl-ACP reductase / FAS-II enoyl-ACP reductase / NADH-dependent 2-trans-enoyl-ACP reductase


Mass: 28524.754 Da / Num. of mol.: 1 / Mutation: T2A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: inhA, Rv1484, MTCY277.05 / Production host: Escherichia coli (E. coli)
References: UniProt: P9WGR1, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-9WE / 1-(pyridin-3-ylmethyl)-3-(1-pyrimidin-2-ylpiperidin-4-yl)urea


Mass: 312.370 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H20N6O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.52 Å3/Da / Density % sol: 65.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 10% glycerol, 25% 1,2propanediol, 0.1M PO4. Cryo is well solution

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 1.71→41.34 Å / Num. obs: 45004 / % possible obs: 99.9 % / Redundancy: 19.2 % / Biso Wilson estimate: 31.31 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.101 / Net I/σ(I): 19.6
Reflection shellResolution: 1.71→1.75 Å / Redundancy: 17.1 % / Rmerge(I) obs: 2.876 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 3248 / CC1/2: 0.514 / % possible all: 100

-
Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
XDSdata reduction
Aimlessdata scaling
BUSTERphasing
RefinementResolution: 1.71→25.04 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.966 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.078 / SU Rfree Blow DPI: 0.073 / SU Rfree Cruickshank DPI: 0.069
RfactorNum. reflection% reflectionSelection details
Rfree0.173 2157 4.8 %RANDOM
Rwork0.16 ---
obs0.161 44906 99.9 %-
Displacement parametersBiso mean: 36.29 Å2
Baniso -1Baniso -2Baniso -3
1--3.398 Å20 Å20 Å2
2---3.398 Å20 Å2
3---6.7959 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: 1 / Resolution: 1.71→25.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1994 0 72 304 2370
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012196HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.993013HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d749SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes46HARMONIC2
X-RAY DIFFRACTIONt_gen_planes343HARMONIC5
X-RAY DIFFRACTIONt_it2196HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.17
X-RAY DIFFRACTIONt_other_torsion14.41
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion288SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2553SEMIHARMONIC4
LS refinement shellResolution: 1.71→1.75 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 171 5.3 %
Rwork0.274 3058 -
all0.274 3229 -
obs--99.5 %
Refinement TLS params.Method: refined / Origin x: 45.8577 Å / Origin y: 48.705 Å / Origin z: -88.9066 Å
111213212223313233
T-0.0925 Å20.0146 Å2-0.013 Å2-0.056 Å20.0368 Å2---0.0401 Å2
L0.5791 °20.0456 °20.0819 °2-0.3907 °2-0.0195 °2--0.8978 °2
S-0.0447 Å °-0.057 Å °0.0315 Å °-0.0017 Å °-0.0467 Å °-0.0998 Å °-0.0716 Å °0.279 Å °0.0914 Å °
Refinement TLS groupSelection details: { A|* }

+
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