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- PDB-4ohu: Crystal structure of Mycobacterium tuberculosis InhA in complex w... -

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Basic information

Entry
Database: PDB / ID: 4ohu
TitleCrystal structure of Mycobacterium tuberculosis InhA in complex with inhibitor PT92
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / catalysis / inhibition / slow-onset inhibition / induced-fit / conformational change / simulation / binding pathway / binding energy / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


enoyl-[acyl-carrier-protein] reductase activity (NAD(P)H) / 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 / fatty acid biosynthetic process ...enoyl-[acyl-carrier-protein] reductase activity (NAD(P)H) / 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 / fatty acid biosynthetic process / 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
2-(2-bromophenoxy)-5-hexylphenol / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Enoyl-[acyl-carrier-protein] reductase [NADH] / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.598 Å
AuthorsLi, H.J. / Pan, P. / Lai, C.T. / Liu, N. / Yu, W. / Garcia-Diaz, M. / Simmerling, C. / Tonge, P.J.
Citation
Journal: Acs Chem.Biol. / Year: 2014
Title: A Structural and Energetic Model for the Slow-Onset Inhibition of the Mycobacterium tuberculosis Enoyl-ACP Reductase InhA.
Authors: Li, H.J. / Lai, C.T. / Pan, P. / Yu, W. / Liu, N. / Bommineni, G.R. / Garcia-Diaz, M. / Simmerling, C. / Tonge, P.J.
#1: Journal: To be Published
Title: Time-dependent diaryl ether inhibitors of InhA: SAR studies of enzyme inhibition, antibacterial activity, and in vivo efficacy
Authors: Pan, P. / Knudson, S. / Bommineni, G.R. / Li, H.J. / Lai, C.T. / Liu, N. / Garcia-Diaz, M. / Simmerling, C. / Patil, S.S. / Slayden, R.A. / Tonge, P.J.
History
DepositionJan 18, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 30, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)126,95512
Polymers122,9054
Non-polymers4,0518
Water7,548419
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18530 Å2
ΔGint-128 kcal/mol
Surface area31820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.845, 90.486, 161.825
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 30726.131 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: inhA, Rv1484, MT1531, MTCY277.05 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: P0A5Y6, UniProt: P9WGR1*PLUS, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-2TK / 2-(2-bromophenoxy)-5-hexylphenol


Mass: 349.262 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H21BrO2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 419 / Source method: isolated from a natural source / Formula: H2O

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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: 2.17 Å3/Da / Density % sol: 43.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 100 mM Bis-tris, 200 mM NaCl, 14% PEG 3350, 4% DMSO, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 5, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 139879 / % possible obs: 98.8 % / Redundancy: 7.1 % / Biso Wilson estimate: 15.25 Å2 / Rmerge(I) obs: 0.084 / Χ2: 1.134 / Net I/σ(I): 15.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.6-1.634.80.31266520.936195.2
1.63-1.665.30.30368790.988197.5
1.66-1.695.90.28168381.005197.8
1.69-1.726.40.26968401.045198
1.72-1.7670.23969091.097198.3
1.76-1.87.50.21768871.168198.3
1.8-1.857.60.18569101.124198.4
1.85-1.97.60.15869241.165198.9
1.9-1.957.60.13969871.234199
1.95-2.027.70.12169671.102198.8
2.02-2.097.60.10769691.121199.3
2.09-2.177.60.09869861.168199.2
2.17-2.277.60.0970471.237199.4
2.27-2.397.60.08570081.256199.6
2.39-2.547.60.08370831.325199.7
2.54-2.747.50.07770791.911199.8
2.74-3.017.50.08171330.821199.8
3.01-3.457.30.07771670.9841100
3.45-4.347.10.0772230.892199.8
4.34-507.20.06473910.89198.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
PHENIX1.7.2_869refinement
PDB_EXTRACT3.14data extraction
CBASSdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2X23

2x23


Resolution: 1.598→28.634 Å / FOM work R set: 0.9006 / SU ML: 0.38 / σ(F): 1.34 / Phase error: 16.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1882 7079 5.07 %
Rwork0.1711 --
obs0.1719 139747 98.44 %
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.66 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 49.38 Å2 / Biso mean: 18.04 Å2 / Biso min: 6.58 Å2
Baniso -1Baniso -2Baniso -3
1-0.4913 Å2-0 Å20 Å2
2---1.4372 Å20 Å2
3---0.9459 Å2
Refinement stepCycle: LAST / Resolution: 1.598→28.634 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7696 0 260 419 8375
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068228
X-RAY DIFFRACTIONf_angle_d1.23111230
X-RAY DIFFRACTIONf_chiral_restr0.0741255
X-RAY DIFFRACTIONf_plane_restr0.0061421
X-RAY DIFFRACTIONf_dihedral_angle_d16.0723098
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5977-1.61580.25531920.22043830402285
1.6158-1.63480.23452080.2114315452397
1.6348-1.65480.24582230.19784347457098
1.6548-1.67570.21492380.18784322456097
1.6757-1.69780.21922510.17764327457898
1.6978-1.7210.19182260.17574354458098
1.721-1.74560.2142110.17384396460798
1.7456-1.77170.21822210.16944392461398
1.7717-1.79930.21382290.16564384461399
1.7993-1.82880.18512570.15614363462099
1.8288-1.86040.17342300.15154391462198
1.8604-1.89420.17242070.1484415462299
1.8942-1.93060.17982480.14924420466899
1.9306-1.970.18442230.15324440466399
1.97-2.01280.1672340.15314414464899
2.0128-2.05970.18012480.15684391463999
2.0597-2.11110.20012460.1644444469099
2.1111-2.16820.18312410.16324428466999
2.1682-2.2320.18312560.15714436469299
2.232-2.3040.16822610.163344474708100
2.304-2.38630.18992550.16344436469199
2.3863-2.48180.21362360.171444784714100
2.4818-2.59470.2032270.183145164743100
2.5947-2.73140.1962240.182245154739100
2.7314-2.90230.20292450.181745194764100
2.9023-3.12620.19252720.18344964768100
3.1262-3.44030.19032170.181745664783100
3.4403-3.9370.17692390.170845774816100
3.937-4.95610.15882550.154246034858100
4.9561-28.6390.18362590.18954706496598
Refinement TLS params.Method: refined / Origin x: 11.491 Å / Origin y: 2.454 Å / Origin z: 59.468 Å
111213212223313233
T0.0647 Å2-0.0024 Å2-0.0145 Å2-0.0997 Å20.0082 Å2--0.068 Å2
L0.3918 °2-0.0296 °2-0.0673 °2-0.8047 °2-0.0398 °2--0.4288 °2
S-0.0099 Å °0.0137 Å °-0.0348 Å °-0.0178 Å °-0.0279 Å °-0.0589 Å °-0.0036 Å °0.0772 Å °0.0342 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:269 OR RESID 300:301 OR RESID 401:502 ) ) OR ( CHAIN C AND ( RESID 2:269 OR RESID 300:301 OR RESID 401:513 ) ) OR ( CHAIN B AND ( RESID 2:269 OR RESID 300:301 OR RESID 401:518 ) ) OR ( CHAIN D AND ( RESID 401:486 OR RESID 3:269 OR RESID 300:301 ) )A3 - 269
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:269 OR RESID 300:301 OR RESID 401:502 ) ) OR ( CHAIN C AND ( RESID 2:269 OR RESID 300:301 OR RESID 401:513 ) ) OR ( CHAIN B AND ( RESID 2:269 OR RESID 300:301 OR RESID 401:518 ) ) OR ( CHAIN D AND ( RESID 401:486 OR RESID 3:269 OR RESID 300:301 ) )A300 - 301
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:269 OR RESID 300:301 OR RESID 401:502 ) ) OR ( CHAIN C AND ( RESID 2:269 OR RESID 300:301 OR RESID 401:513 ) ) OR ( CHAIN B AND ( RESID 2:269 OR RESID 300:301 OR RESID 401:518 ) ) OR ( CHAIN D AND ( RESID 401:486 OR RESID 3:269 OR RESID 300:301 ) )A401 - 502
4X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:269 OR RESID 300:301 OR RESID 401:502 ) ) OR ( CHAIN C AND ( RESID 2:269 OR RESID 300:301 OR RESID 401:513 ) ) OR ( CHAIN B AND ( RESID 2:269 OR RESID 300:301 OR RESID 401:518 ) ) OR ( CHAIN D AND ( RESID 401:486 OR RESID 3:269 OR RESID 300:301 ) )C2 - 269
5X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:269 OR RESID 300:301 OR RESID 401:502 ) ) OR ( CHAIN C AND ( RESID 2:269 OR RESID 300:301 OR RESID 401:513 ) ) OR ( CHAIN B AND ( RESID 2:269 OR RESID 300:301 OR RESID 401:518 ) ) OR ( CHAIN D AND ( RESID 401:486 OR RESID 3:269 OR RESID 300:301 ) )C300 - 301
6X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:269 OR RESID 300:301 OR RESID 401:502 ) ) OR ( CHAIN C AND ( RESID 2:269 OR RESID 300:301 OR RESID 401:513 ) ) OR ( CHAIN B AND ( RESID 2:269 OR RESID 300:301 OR RESID 401:518 ) ) OR ( CHAIN D AND ( RESID 401:486 OR RESID 3:269 OR RESID 300:301 ) )C401 - 513
7X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:269 OR RESID 300:301 OR RESID 401:502 ) ) OR ( CHAIN C AND ( RESID 2:269 OR RESID 300:301 OR RESID 401:513 ) ) OR ( CHAIN B AND ( RESID 2:269 OR RESID 300:301 OR RESID 401:518 ) ) OR ( CHAIN D AND ( RESID 401:486 OR RESID 3:269 OR RESID 300:301 ) )B2 - 269
8X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:269 OR RESID 300:301 OR RESID 401:502 ) ) OR ( CHAIN C AND ( RESID 2:269 OR RESID 300:301 OR RESID 401:513 ) ) OR ( CHAIN B AND ( RESID 2:269 OR RESID 300:301 OR RESID 401:518 ) ) OR ( CHAIN D AND ( RESID 401:486 OR RESID 3:269 OR RESID 300:301 ) )B300 - 301
9X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:269 OR RESID 300:301 OR RESID 401:502 ) ) OR ( CHAIN C AND ( RESID 2:269 OR RESID 300:301 OR RESID 401:513 ) ) OR ( CHAIN B AND ( RESID 2:269 OR RESID 300:301 OR RESID 401:518 ) ) OR ( CHAIN D AND ( RESID 401:486 OR RESID 3:269 OR RESID 300:301 ) )B401 - 518
10X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:269 OR RESID 300:301 OR RESID 401:502 ) ) OR ( CHAIN C AND ( RESID 2:269 OR RESID 300:301 OR RESID 401:513 ) ) OR ( CHAIN B AND ( RESID 2:269 OR RESID 300:301 OR RESID 401:518 ) ) OR ( CHAIN D AND ( RESID 401:486 OR RESID 3:269 OR RESID 300:301 ) )D401 - 486
11X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:269 OR RESID 300:301 OR RESID 401:502 ) ) OR ( CHAIN C AND ( RESID 2:269 OR RESID 300:301 OR RESID 401:513 ) ) OR ( CHAIN B AND ( RESID 2:269 OR RESID 300:301 OR RESID 401:518 ) ) OR ( CHAIN D AND ( RESID 401:486 OR RESID 3:269 OR RESID 300:301 ) )D3 - 269
12X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:269 OR RESID 300:301 OR RESID 401:502 ) ) OR ( CHAIN C AND ( RESID 2:269 OR RESID 300:301 OR RESID 401:513 ) ) OR ( CHAIN B AND ( RESID 2:269 OR RESID 300:301 OR RESID 401:518 ) ) OR ( CHAIN D AND ( RESID 401:486 OR RESID 3:269 OR RESID 300:301 ) )D300 - 301

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