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- PDB-8pa9: Crystal structure of human Histidine Triad Nucleotide-Binding Pro... -

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Basic information

Entry
Database: PDB / ID: 8pa9
TitleCrystal structure of human Histidine Triad Nucleotide-Binding Protein 1 in complex with 5'-O-[(3-Indolyl)-1-Ethyl]Carbamoyl N2-methyl-2-aminoethenoadenosine
ComponentsHistidine triad nucleotide-binding protein 1
KeywordsHYDROLASE / HINT / HIT / histidine triad / phosphoramidase / complex / inhibitor
Function / homology
Function and homology information


purine ribonucleotide catabolic process / Hydrolases; Acting on phosphorus-nitrogen bonds / adenosine 5'-monophosphoramidase activity / deSUMOylase activity / protein desumoylation / Regulation of MITF-M-dependent genes involved in apoptosis / histone deacetylase complex / intrinsic apoptotic signaling pathway by p53 class mediator / Transcriptional and post-translational regulation of MITF-M expression and activity / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation ...purine ribonucleotide catabolic process / Hydrolases; Acting on phosphorus-nitrogen bonds / adenosine 5'-monophosphoramidase activity / deSUMOylase activity / protein desumoylation / Regulation of MITF-M-dependent genes involved in apoptosis / histone deacetylase complex / intrinsic apoptotic signaling pathway by p53 class mediator / Transcriptional and post-translational regulation of MITF-M expression and activity / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / positive regulation of calcium-mediated signaling / protein kinase C binding / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / cytoskeleton / hydrolase activity / nucleotide binding / regulation of DNA-templated transcription / signal transduction / proteolysis / extracellular exosome / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Histidine triad (HIT) protein / HIT domain / Histidine triad, conserved site / HIT domain signature. / HIT domain profile. / HIT-like domain / HIT-like superfamily
Similarity search - Domain/homology
Chem-XKF / Adenosine 5'-monophosphoramidase HINT1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsDolot, R.M. / Dillenburg, M. / Wagner, C.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI146049 United States
CitationJournal: To Be Published
Title: Novel inhibitors for hHINT1 protein
Authors: Dillenburg, M. / Dolot, R. / Wagner, C.R.
History
DepositionJun 7, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histidine triad nucleotide-binding protein 1
B: Histidine triad nucleotide-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1543
Polymers27,6482
Non-polymers5071
Water5,981332
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3880 Å2
ΔGint-16 kcal/mol
Surface area9570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.597, 46.314, 64.010
Angle α, β, γ (deg.)90.000, 94.707, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Histidine triad nucleotide-binding protein 1 / Adenosine 5'-monophosphoramidase / Protein kinase C inhibitor 1 / Protein kinase C-interacting ...Adenosine 5'-monophosphoramidase / Protein kinase C inhibitor 1 / Protein kinase C-interacting protein 1 / PKCI-1


Mass: 13823.931 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HINT1, HINT, PKCI1, PRKCNH1 / Plasmid: pSGA02 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P49773, Hydrolases
#2: Chemical ChemComp-XKF / 5'-O-[(3-Indolyl)-1-Ethyl]Carbamoyl N2-methyl-2-aminoethenoadenosine / [(2~{R},3~{S},4~{R},5~{R})-5-[5-(methylamino)imidazo[2,1-f]purin-3-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-[2-(1~{H}-indol-3-yl)ethyl]carbamate


Mass: 506.514 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H26N8O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.1 Å3/Da / Density % sol: 41.42 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 12% w/v PEG4000, 0.1 M sodium cacodylate pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU PhotonJet-S / Wavelength: 1.54184 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Feb 9, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 1.5→18.451 Å / Num. obs: 36820 / % possible obs: 99.8 % / Redundancy: 5.1 % / Biso Wilson estimate: 9 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.028 / Rrim(I) all: 0.068 / Χ2: 0.95 / Net I/σ(I): 14.2
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.503 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1815 / CC1/2: 0.84 / Rpim(I) all: 0.315 / Rrim(I) all: 0.598 / Χ2: 1.03 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
CrysalisPro1.171.42.80adata reduction
Aimless0.7.9data scaling
MOLREP11.9.02phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→18.451 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.429 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.07 / ESU R Free: 0.072
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1794 1878 5.101 %
Rwork0.149 34937 -
all0.151 --
obs-36815 99.702 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 11.513 Å2
Baniso -1Baniso -2Baniso -3
1-1.353 Å20 Å2-0.171 Å2
2---0.48 Å2-0 Å2
3----0.834 Å2
Refinement stepCycle: LAST / Resolution: 1.5→18.451 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1762 0 37 332 2131
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0122154
X-RAY DIFFRACTIONr_bond_other_d0.0020.0161983
X-RAY DIFFRACTIONr_angle_refined_deg1.6571.6522959
X-RAY DIFFRACTIONr_angle_other_deg0.6061.6054627
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.145283
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.742516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.72110368
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.7151090
X-RAY DIFFRACTIONr_chiral_restr0.0930.2306
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022607
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02463
X-RAY DIFFRACTIONr_nbd_refined0.2320.2460
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2010.21927
X-RAY DIFFRACTIONr_nbtor_refined0.1770.21079
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.21136
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1950.2227
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2640.221
X-RAY DIFFRACTIONr_nbd_other0.1560.253
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.20.233
X-RAY DIFFRACTIONr_mcbond_it1.2131.041057
X-RAY DIFFRACTIONr_mcbond_other1.211.041056
X-RAY DIFFRACTIONr_mcangle_it1.9341.8671365
X-RAY DIFFRACTIONr_mcangle_other1.9331.8671366
X-RAY DIFFRACTIONr_scbond_it1.8771.3261097
X-RAY DIFFRACTIONr_scbond_other1.8771.3261097
X-RAY DIFFRACTIONr_scangle_it2.8812.3321594
X-RAY DIFFRACTIONr_scangle_other2.882.3321595
X-RAY DIFFRACTIONr_lrange_it5.05115.0922700
X-RAY DIFFRACTIONr_lrange_other4.72112.3292593
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.5-1.5390.2521360.2325270.23126980.9550.95698.70270.2
1.539-1.5810.2441420.20824840.2126490.9550.96599.13170.178
1.581-1.6260.2311250.18424260.18725560.970.97499.80440.157
1.626-1.6760.1831200.18323430.18324700.9790.97599.71660.154
1.676-1.730.2451170.17322900.17624070.9580.9791000.146
1.73-1.790.2191120.16722210.1723330.9710.9811000.14
1.79-1.8570.1851090.15821420.15922510.9760.9831000.133
1.857-1.9320.178900.14820800.14921710.9790.98599.95390.126
1.932-2.0170.1721060.14219790.14420850.9810.9871000.125
2.017-2.1140.1891110.13918780.14219890.9760.9881000.126
2.114-2.2270.1551030.12818010.12919040.9850.991000.116
2.227-2.360.135840.11317070.11417910.9870.9921000.104
2.36-2.520.17830.13316220.13517060.9830.98999.94140.121
2.52-2.7180.226710.14415170.14815880.9660.9871000.136
2.718-2.9710.201840.13113600.13514440.9780.9891000.126
2.971-3.3110.163820.13412680.13513500.9840.9891000.131
3.311-3.8020.173840.13611110.13911960.9820.9999.91640.139
3.802-4.6080.091480.1189580.11610080.9940.99299.80160.124
4.608-6.3230.185470.1647520.1658000.9860.98799.8750.168
6.323-18.4510.136240.1964720.1925030.9880.97998.60840.207

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