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

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Basic information

Entry
Database: PDB / ID: 8pai
TitleCrystal structure of human Histidine Triad Nucleotide-Binding Protein 1 in complex with 5'-O-[N-(3-Indolepropionic acid)sulfamoyl] 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 / adenylylsulfatase activity / Hydrolases; Acting on phosphorus-nitrogen bonds / adenosine 5'-monophosphoramidase activity / deSUMOylase activity / protein desumoylation / sulfur compound metabolic process / histone deacetylase complex / intrinsic apoptotic signaling pathway by p53 class mediator / positive regulation of calcium-mediated signaling ...purine ribonucleotide catabolic process / adenylylsulfatase activity / Hydrolases; Acting on phosphorus-nitrogen bonds / adenosine 5'-monophosphoramidase activity / deSUMOylase activity / protein desumoylation / sulfur compound metabolic process / histone deacetylase complex / intrinsic apoptotic signaling pathway by p53 class mediator / 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 / cytoplasm / cytosol
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-XKO / Adenosine 5'-monophosphoramidase HINT1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 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

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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)28,2183
Polymers27,6482
Non-polymers5711
Water4,288238
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-14 kcal/mol
Surface area9620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.675, 46.434, 63.788
Angle α, β, γ (deg.)90.000, 94.624, 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-XKO / 5'-O-[N-(3-Indolepropionic acid)sulfamoyl] 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}-[3-(1~{H}-indol-3-yl)propanoyl]sulfamate


Mass: 570.578 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H26N8O7S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 2.07 Å3/Da / Density % sol: 40.68 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 10% 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 10, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 1.8→19.041 Å / Num. obs: 21127 / % possible obs: 99.8 % / Redundancy: 5.7 % / Biso Wilson estimate: 10 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.039 / Rrim(I) all: 0.096 / Χ2: 0.97 / Net I/σ(I): 12.6
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.369 / Num. unique obs: 1216 / CC1/2: 0.893 / Rpim(I) all: 0.226 / Rrim(I) all: 0.435 / Χ2: 0.84 / % possible all: 99.8

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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: 1.8→19.041 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.504 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.115
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1906 982 4.651 %
Rwork0.1494 20130 -
all0.151 --
obs-21112 99.688 %
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: 13.439 Å2
Baniso -1Baniso -2Baniso -3
1-1.55 Å20 Å2-0.247 Å2
2---0.729 Å20 Å2
3----0.771 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.041 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1767 0 40 238 2045
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0122006
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161878
X-RAY DIFFRACTIONr_angle_refined_deg1.5281.6582737
X-RAY DIFFRACTIONr_angle_other_deg0.5311.6024368
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.635257
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.732512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.20710344
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.4981086
X-RAY DIFFRACTIONr_chiral_restr0.0780.2286
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022377
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02432
X-RAY DIFFRACTIONr_nbd_refined0.2240.2419
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1960.21795
X-RAY DIFFRACTIONr_nbtor_refined0.1730.2976
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.21067
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2155
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2050.215
X-RAY DIFFRACTIONr_nbd_other0.1460.252
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2010.215
X-RAY DIFFRACTIONr_mcbond_it1.2591.235989
X-RAY DIFFRACTIONr_mcbond_other1.2561.234988
X-RAY DIFFRACTIONr_mcangle_it1.9732.2131259
X-RAY DIFFRACTIONr_mcangle_other1.9722.2121260
X-RAY DIFFRACTIONr_scbond_it2.2051.5571017
X-RAY DIFFRACTIONr_scbond_other2.2051.5571017
X-RAY DIFFRACTIONr_scangle_it3.3322.7561478
X-RAY DIFFRACTIONr_scangle_other3.332.7561479
X-RAY DIFFRACTIONr_lrange_it5.81115.2422366
X-RAY DIFFRACTIONr_lrange_other5.59814.0182317
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
1.8-1.8460.223780.19214430.19415240.970.97599.80310.17
1.846-1.8960.259680.17514310.17915000.9610.97799.93330.149
1.896-1.9510.204810.1613880.16214700.9750.98399.9320.136
1.951-2.010.183770.15713380.15914150.9760.9831000.134
2.01-2.0750.227680.15212960.15613650.9670.98599.92670.132
2.075-2.1470.205640.15212930.15513580.9780.98699.92640.132
2.147-2.2270.165590.13712210.13812800.9830.9881000.122
2.227-2.3170.193590.13111890.13412500.9780.98999.840.115
2.317-2.4180.166590.12811370.1311970.9810.9999.91650.114
2.418-2.5340.17480.13810890.1411370.9810.9881000.12
2.534-2.6690.195530.14210350.14410890.980.98899.90820.125
2.669-2.8270.195450.1369910.13910360.980.9891000.121
2.827-3.0180.251360.1379450.1419810.9630.9881000.128
3.018-3.2530.155350.1418730.1419080.9850.9881000.133
3.253-3.5530.175280.1457990.1468330.9830.98799.27970.138
3.553-3.9550.151330.1467310.1467660.9860.98899.73890.145
3.955-4.5340.161260.1286570.136900.9890.9998.98550.128
4.534-5.4760.171240.1695500.1695800.980.98698.96550.166
5.476-7.4430.236360.2194380.2214740.9670.9761000.218
7.443-19.0410.27450.1892860.1913020.9840.98196.35760.198

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