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- PDB-9md7: Hip1 complex with inhibitor #1 (Hip1-1) via Ser228 -

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Basic information

Entry
Database: PDB / ID: 9md7
TitleHip1 complex with inhibitor #1 (Hip1-1) via Ser228
ComponentsProtease
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Tuberculosis / protease inhibitor / Rv2224c/caeA/hip1 / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Dipeptidyl-peptidases and tripeptidyl-peptidases / Hydrolases; Acting on peptide bonds (peptidases) / peptidase activity / proteolysis
Similarity search - Function
: / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.72 Å
AuthorsYim, M.K. / Olsen, K.J. / Brooks, C.L. / Pena, K.J. / Johnson, S.J. / Goldfarb, N.E.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: To Be Published
Title: Discovery of Highly Potent alpha-Keto Ester-Based Peptidomimetic Inhibitors of the Hip1 Protease for the Treatment of Mycobacterium tuberculosis
Authors: Schumann, N.C. / Harris, H.T. / Rouse Salcido, E.M. / Brooks, C.L. / Pena, K.J. / Karakousis, P.C. / Abell, A.D. / Olsen, K.J. / Yim, M.K. / Johnson, S.J. / Goldfarb, N.E.
History
DepositionDec 5, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 17, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7142
Polymers52,2171
Non-polymers4971
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.333, 104.333, 129.125
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Protein Protease


Mass: 52217.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: tap, ERS007688_01841 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A654TLU9, Hydrolases; Acting on peptide bonds (peptidases), Hydrolases; Acting on peptide bonds (peptidases); Dipeptidyl-peptidases and tripeptidyl-peptidases
#2: Chemical ChemComp-A1BK4 / N-(dihydroxymethyl)-L-phenylalanyl-N-[(2R,3S)-2-hydroxy-1-methoxy-5-methyl-1-oxohexan-3-yl]-L-lysinamide / methyl (5S,8S,11S)-8-(4-aminobutyl)-5-benzyl-11-isobutyl-3,6,9,12-tetraoxo-1-phenyl-2-oxa-4,7,10-triazatridecan-13-oate bound form


Mass: 496.597 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C24H40N4O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 4.07 Å3/Da / Density % sol: 69.75 % / Description: Large rods
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25.5% PEG 8000, 0.12 M ammonium Sulfate, 0.085 M Na Cacodylate trihydrate, pH 6.5, 15% v/v glycerol

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Oxford Cryojet / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.21
ReflectionResolution: 2.72→48.37 Å / Num. obs: 22359 / % possible obs: 99.47 % / Redundancy: 15.4 % / CC1/2: 0.971 / CC star: 0.993 / Χ2: 1.031 / Net I/σ(I): 7.27
Reflection shellResolution: 2.72→2.8 Å / Redundancy: 7.4 % / Num. unique obs: 2204 / CC1/2: 0.354 / CC star: 0.723 / Χ2: 0.986 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
HKL-3000data scaling
PHENIX1.21.2_5419phasing
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.72→48.37 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.4392
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2593 2015 9.03 %
Rwork0.2189 20290 -
obs0.2262 22305 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.96 Å2
Refinement stepCycle: LAST / Resolution: 2.72→48.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3507 0 36 2 3545
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00873625
X-RAY DIFFRACTIONf_angle_d0.93754941
X-RAY DIFFRACTIONf_chiral_restr0.048541
X-RAY DIFFRACTIONf_plane_restr0.0083664
X-RAY DIFFRACTIONf_dihedral_angle_d18.87041333
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.72-2.780.35041330.31971342X-RAY DIFFRACTION85.92
2.78-2.860.34461430.31321442X-RAY DIFFRACTION90.63
2.86-2.940.34661390.32931426X-RAY DIFFRACTION90.83
2.94-3.040.31781390.321418X-RAY DIFFRACTION90.84
3.04-3.150.35161440.30311455X-RAY DIFFRACTION90.71
3.15-3.270.3131410.27791445X-RAY DIFFRACTION91.05
3.27-3.420.29151380.25821430X-RAY DIFFRACTION91.2
3.42-3.60.31311490.24461456X-RAY DIFFRACTION90.72
3.6-3.830.27311460.22471443X-RAY DIFFRACTION90.7
3.83-4.120.27841450.19891454X-RAY DIFFRACTION90.88
4.12-4.540.21951430.18871469X-RAY DIFFRACTION91.13
4.54-5.190.17581460.17031471X-RAY DIFFRACTION90.91
5.2-6.540.25021480.20061486X-RAY DIFFRACTION90.94
6.54-48.370.23671570.1831557X-RAY DIFFRACTION90.47
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)
13.794764625881.32634252761.485307340671.686923204740.530998758071.570595668370.02112213675670.03932038465770.3630754530580.0291829082306-0.1086953892370.410762268268-0.025892411811-0.01274261534960.09974447465390.413435560012-0.0174108672805-0.001768584161690.3305692429710.04320743762730.39604259659726.7627778276-28.851529562-3.23333728698
22.605299563110.607246937005-0.4066369388291.868110177020.07043762638211.575341445640.0309051714120.07151984983170.147229549283-0.178438837436-0.1029528694710.0763662731875-0.3432918871110.1561895029860.07926359852840.410109747838-0.00939011207416-0.07344460470720.3845614269520.02880655491770.293995277151.8262273766-28.5899272995-5.50378717927
33.224866041571.070359700770.936810927062.201791728270.4230164615290.5289972947870.07798242009570.0509976413722-0.228640334562-0.0436405094674-0.00212866982944-0.09240211872940.2084177008090.0989915936509-0.05215354388010.466187800793-0.0103909973785-0.01641457464340.3927473739690.0671482614740.31621278440238.2145989317-42.6262662275-2.16476929272
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 49 through 259 )49 - 2591 - 203
22chain 'A' and (resid 260 through 401 )260 - 401204 - 345
33chain 'A' and (resid 402 through 520 )402 - 520346 - 464

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