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- PDB-5i2f: Human Histidine Triad Nucleotide Binding Protein 1 (hHint1) with ... -

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Basic information

Entry
Database: PDB / ID: 5i2f
TitleHuman Histidine Triad Nucleotide Binding Protein 1 (hHint1) with bound sulfamide inhibitor Bio-AMS
ComponentsHistidine triad nucleotide-binding protein 1
KeywordsHydrolase/Hydrolase Inhibitor / HINT / histidine triad / HIT / Hydrolase Inhibitor complex / Hydrolase-Hydrolase Inhibitor complex
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 / HIT family, subunit A / HIT-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-BS5 / Adenosine 5'-monophosphoramidase HINT1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsMaize, K.M. / Finzel, B.C.
CitationJournal: Acs Med.Chem.Lett. / Year: 2016
Title: Design, Synthesis, and Characterization of Sulfamide and Sulfamate Nucleotidomimetic Inhibitors of hHint1.
Authors: Shah, R. / Strom, A. / Zhou, A. / Maize, K.M. / Finzel, B.C. / Wagner, C.R.
History
DepositionFeb 8, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2016Group: Database references
Revision 1.2Sep 27, 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 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)28,8885
Polymers28,1922
Non-polymers6963
Water4,684260
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-13 kcal/mol
Surface area9640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.493, 46.314, 64.073
Angle α, β, γ (deg.)90.000, 94.440, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-413-

HOH

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Components

#1: Protein Histidine triad nucleotide-binding protein 1 / Adenosine 5'-monophosphoramidase


Mass: 14096.188 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HINT1, HINT / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 pLysS / References: UniProt: P49773, Hydrolases
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-BS5 / 5'-deoxy-5'-[({5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoyl}sulfamoyl)amino]adenosine


Mass: 571.630 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H29N9O7S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 2.03 Å3/Da / Density % sol: 39.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.9 / Details: 100 mM MES, 33% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.25→39.724 Å / Num. obs: 61412 / % possible obs: 97.9 % / Redundancy: 3.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.027 / Rpim(I) all: 0.017 / Rrim(I) all: 0.032 / Net I/σ(I): 24.1 / Num. measured all: 203409
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.3 % / Rejects: _

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.25-1.2540.13320306190.9820.0870.1597.694.9
5.796-39.7240.02321526530.9980.0150.02846.797.5

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Processing

Software
NameVersionClassification
REFMACrefinement
PDB_EXTRACT3.15data extraction
PHASERphasing
SCALAdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TW2

3tw2


Resolution: 1.25→31.94 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1751 3117 5.08 %
Rwork0.1554 --
obs0.1564 61404 97.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 54.61 Å2 / Biso mean: 14.8305 Å2 / Biso min: 6.18 Å2
Refinement stepCycle: final / Resolution: 1.25→31.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1767 0 34 260 2061
Biso mean--23.24 26.13 -
Num. residues----228

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