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- PDB-9gyp: Crystal structure of human Histidine Triad Nucleotide-Binding Pro... -

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Basic information

Entry
Database: PDB / ID: 9gyp
TitleCrystal structure of human Histidine Triad Nucleotide-Binding Protein 1 in complex with KV24
ComponentsHistidine triad nucleotide-binding protein 1
KeywordsHYDROLASE / ligand binding / histidine triad / nucleotide binding / HIT protein
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 / intrinsic apoptotic signaling pathway by p53 class mediator / histone deacetylase complex / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / Transcriptional and post-translational regulation of MITF-M expression and activity ...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 / intrinsic apoptotic signaling pathway by p53 class mediator / histone deacetylase complex / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / Transcriptional and post-translational regulation of MITF-M expression and activity / positive regulation of calcium-mediated signaling / protein kinase C binding / cytoskeleton / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / 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
: / Adenosine 5'-monophosphoramidase HINT1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.801 Å
AuthorsDolot, R.M. / Lechner, S. / Sethiya, J.P. / Wagner, C.R. / Bracher, F. / Kuster, B.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB1309 Germany
CitationJournal: Acs Chem.Biol. / Year: 2025
Title: Serendipitous and Systematic Chemoproteomic Discovery of MBLAC2, HINT1, and NME1-4 Inhibitors from Histone Deacetylase-Targeting Pharmacophores.
Authors: Lechner, S. / Sha, S. / Sethiya, J.P. / Szczupak, P. / Dolot, R. / Lomada, S. / Sakhteman, A. / Tushaus, J. / Prokofeva, P. / Krauss, M. / Breu, F. / Vogerl, K. / Morgenstern, M. / Hrabe de ...Authors: Lechner, S. / Sha, S. / Sethiya, J.P. / Szczupak, P. / Dolot, R. / Lomada, S. / Sakhteman, A. / Tushaus, J. / Prokofeva, P. / Krauss, M. / Breu, F. / Vogerl, K. / Morgenstern, M. / Hrabe de Angelis, M. / Haucke, V. / Wieland, T. / Wagner, C. / Medard, G. / Bracher, F. / Kuster, B.
History
DepositionOct 2, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 2, 2025Provider: repository / Type: Initial release

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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)28,1445
Polymers27,6482
Non-polymers4963
Water4,684260
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-55 kcal/mol
Surface area9490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.957, 46.446, 63.788
Angle α, β, γ (deg.)90.000, 94.533, 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-A1IQU / ~{N}-oxidanyl-4-(5~{H}-pyrrolo[1,2-a]quinoxalin-4-yl)benzamide


Mass: 304.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H14N3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.08 Å3/Da / Density % sol: 40.92 %
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: Dec 14, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 1.8→18.416 Å / Num. obs: 21094 / % possible obs: 99.3 % / Redundancy: 3.8 % / Biso Wilson estimate: 12.3 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.032 / Rrim(I) all: 0.065 / Χ2: 0.93 / Net I/σ(I): 15.1
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 1233 / CC1/2: 0.874 / Rpim(I) all: 0.251 / Rrim(I) all: 0.428 / Χ2: 0.95 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
CrysalisPro43.100adata reduction
Aimless0.7.13data scaling
MOLREP11.9.02phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.801→18.416 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.614 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.116
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1908 981 4.656 %
Rwork0.141 20088 -
all0.143 --
obs-21069 99.144 %
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: 15.055 Å2
Baniso -1Baniso -2Baniso -3
1-1.808 Å20 Å2-0.363 Å2
2---0.344 Å20 Å2
3----1.389 Å2
Refinement stepCycle: LAST / Resolution: 1.801→18.416 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1762 0 33 260 2055
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0121991
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161855
X-RAY DIFFRACTIONr_angle_refined_deg1.6511.8152716
X-RAY DIFFRACTIONr_angle_other_deg0.5871.7944311
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5185258
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.627510
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.01310344
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.3151087
X-RAY DIFFRACTIONr_chiral_restr0.0840.2284
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022389
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02431
X-RAY DIFFRACTIONr_nbd_refined0.2180.2412
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1990.21762
X-RAY DIFFRACTIONr_nbtor_refined0.1720.2974
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.21042
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.2176
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1140.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1150.217
X-RAY DIFFRACTIONr_nbd_other0.1580.255
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1990.222
X-RAY DIFFRACTIONr_mcbond_it1.291.44990
X-RAY DIFFRACTIONr_mcbond_other1.2891.439989
X-RAY DIFFRACTIONr_mcangle_it1.982.5821262
X-RAY DIFFRACTIONr_mcangle_other1.982.5811263
X-RAY DIFFRACTIONr_scbond_it2.311.7211001
X-RAY DIFFRACTIONr_scbond_other2.0051.716993
X-RAY DIFFRACTIONr_scangle_it3.2543.0591454
X-RAY DIFFRACTIONr_scangle_other3.1823.041443
X-RAY DIFFRACTIONr_lrange_it5.34617.4782357
X-RAY DIFFRACTIONr_lrange_other5.10515.7662294
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
1.801-1.8470.221750.19414500.19515440.9720.97398.76940.169
1.847-1.8970.294720.17814260.18415150.9530.97498.87790.149
1.897-1.9520.195800.16713670.16914610.970.9899.04180.141
1.952-2.0110.216730.16413340.16714220.9610.98298.94510.136
2.011-2.0760.23720.16112870.16413750.9650.98298.83640.134
2.076-2.1480.196630.14712650.14913430.980.98698.88310.126
2.148-2.2280.154570.13712250.13812900.9840.98799.37980.115
2.228-2.3180.193600.12111800.12412400.9770.991000.103
2.318-2.4190.14540.11911480.1212020.9870.9911000.103
2.419-2.5350.184520.12611030.12911550.9810.991000.109
2.535-2.6690.184560.1310300.13310860.9820.9891000.113
2.669-2.8270.223450.149880.14410330.9650.9881000.126
2.827-3.0180.23350.1419530.1439880.970.9871000.13
3.018-3.2520.209340.1348750.1369100.9740.98999.89010.126
3.252-3.5510.162300.1358020.1368370.9840.9999.40260.131
3.551-3.9520.165310.1357240.1377660.9850.98998.5640.137
3.952-4.5290.158260.1166560.1176910.9880.99198.69750.118
4.529-5.4650.138260.1285470.1295820.990.99298.45360.13
5.465-7.4090.226340.1694310.1734710.9840.98598.72610.164
7.409-18.4160.17560.1612930.1613090.9920.98696.76380.167

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