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- PDB-5km8: Human Histidine Triad Nucleotide Binding Protein 2 (hHint2) Cidof... -

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Basic information

Entry
Database: PDB / ID: 5km8
TitleHuman Histidine Triad Nucleotide Binding Protein 2 (hHint2) Cidofovir complex
ComponentsHistidine triad nucleotide-binding protein 2, mitochondrial
KeywordsHYDROLASE / HINT / histidine triad / HIT
Function / homology
Function and homology information


Hydrolases; Acting on phosphorus-nitrogen bonds / adenosine 5'-monophosphoramidase activity / steroid biosynthetic process / RHOD GTPase cycle / lipid catabolic process / mitochondrial outer membrane / hydrolase activity / mitochondrial matrix / nucleotide binding / apoptotic process ...Hydrolases; Acting on phosphorus-nitrogen bonds / adenosine 5'-monophosphoramidase activity / steroid biosynthetic process / RHOD GTPase cycle / lipid catabolic process / mitochondrial outer membrane / hydrolase activity / mitochondrial matrix / nucleotide binding / apoptotic process / mitochondrion / 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 / HIT family, subunit A / HIT-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-L8P / Adenosine 5'-monophosphoramidase HINT2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsMaize, K.M. / Finzel, B.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM08700 United States
CitationJournal: Mol. Pharm. / Year: 2017
Title: A Crystal Structure Based Guide to the Design of Human Histidine Triad Nucleotide Binding Protein 1 (hHint1) Activated ProTides.
Authors: Maize, K.M. / Shah, R. / Strom, A. / Kumarapperuma, S. / Zhou, A. / Wagner, C.R. / Finzel, B.C.
History
DepositionJun 26, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2017Group: Author supporting evidence / Database references / Category: citation_author / pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 18, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Nov 15, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support
Item: _citation.country / _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histidine triad nucleotide-binding protein 2, mitochondrial
B: Histidine triad nucleotide-binding protein 2, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0528
Polymers30,4432
Non-polymers6096
Water1,856103
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5040 Å2
ΔGint-26 kcal/mol
Surface area9260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.990, 73.852, 77.464
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Histidine triad nucleotide-binding protein 2, mitochondrial / HINT-2 / HINT-3 / HIT-17kDa


Mass: 15221.329 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HINT2 / Plasmid: pMCSG9 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 pLysS / References: UniProt: Q9BX68, Hydrolases

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Non-polymers , 6 types, 109 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-L8P / ({[(2S)-1-(4-amino-2-oxopyrimidin-1(2H)-yl)-3-hydroxypropan-2-yl]oxy}methyl)phosphonic acid / Cidofovir


Mass: 279.187 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H14N3O6P
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 1.78 Å3/Da / Density % sol: 31.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 100 mM MES, 45% 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: Dec 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→77.464 Å / Num. obs: 15330 / % possible obs: 100 % / Redundancy: 6.2 % / Biso Wilson estimate: 25.29 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.029 / Rrim(I) all: 0.073 / Net I/σ(I): 19.1 / Num. measured all: 94866
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2-2.0076.20.4011100
9.278-77.46450.0311100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.31 Å36.93 Å
Translation5.31 Å36.93 Å

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.14data extraction
PHASERphasing
SCALAdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4inc

4inc


Resolution: 2→36.926 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.59
RfactorNum. reflection% reflection
Rfree0.2125 766 5.01 %
Rwork0.1607 --
obs0.1631 15284 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 59.42 Å2 / Biso mean: 26.0636 Å2 / Biso min: 13.17 Å2
Refinement stepCycle: final / Resolution: 2→36.926 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1651 0 37 103 1791
Biso mean--37 34.72 -
Num. residues----214
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081723
X-RAY DIFFRACTIONf_angle_d1.1712341
X-RAY DIFFRACTIONf_chiral_restr0.055261
X-RAY DIFFRACTIONf_plane_restr0.005304
X-RAY DIFFRACTIONf_dihedral_angle_d13.611637
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2-2.15440.2341430.174728332976
2.1544-2.37120.23091840.16328363020
2.3712-2.71420.20791470.166328773024
2.7142-3.41930.22051510.168729063057
3.4193-36.93230.19621410.151130663207

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