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- PDB-8hu6: AMP deaminase 2 in complex with AMP -

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Basic information

Entry
Database: PDB / ID: 8hu6
TitleAMP deaminase 2 in complex with AMP
ComponentsAMP deaminase 2
KeywordsHYDROLASE / Complex / Deaminase / AMP / IMP / Energy metabolism
Function / homology
Function and homology information


cyclic purine nucleotide metabolic process / AMP deaminase / AMP deaminase activity / IMP biosynthetic process / AMP metabolic process / Purine salvage / IMP salvage / energy homeostasis / identical protein binding / metal ion binding / cytosol
Similarity search - Function
AMP deaminase / AMP deaminase / Adenosine/AMP deaminase active site / Adenosine and AMP deaminase signature. / Metal-dependent hydrolase
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / AMP deaminase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsAdachi, T. / Doi, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2023
Title: The discovery of 3,3-dimethyl-1,2,3,4-tetrahydroquinoxaline-1-carboxamides as AMPD2 inhibitors with a novel mechanism of action.
Authors: Kitao, Y. / Saito, T. / Watanabe, S. / Ohe, Y. / Takahashi, K. / Akaki, T. / Adachi, T. / Doi, S. / Yamanaka, K. / Murai, Y. / Oba, M. / Suzuki, T.
History
DepositionDec 22, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID
Revision 1.2May 29, 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: AMP deaminase 2
B: AMP deaminase 2
C: AMP deaminase 2
D: AMP deaminase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)316,00413
Polymers315,0114
Non-polymers9939
Water14,052780
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17430 Å2
ΔGint-265 kcal/mol
Surface area90180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.665, 163.563, 289.385
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein
AMP deaminase 2 / AMP deaminase isoform L


Mass: 78752.648 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AMPD2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q01433, AMP deaminase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 780 / 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: 2.32 Å3/Da / Density % sol: 47.04 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 5.9
Details: 85 mM MES ph 5.9, 20% PEG8000, 170 mM ammonium sulfate, 15% glycerol, 10mM AMP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 27, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.33→289.39 Å / Num. obs: 122956 / % possible obs: 99 % / Redundancy: 4.1 % / Biso Wilson estimate: 35.54 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.049 / Rrim(I) all: 0.094 / Net I/σ(I): 12.1
Reflection shellResolution: 2.33→2.39 Å / Rmerge(I) obs: 0.373 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 8943 / CC1/2: 0.91 / Rpim(I) all: 0.189 / Rrim(I) all: 0.42

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Processing

Software
NameVersionClassification
DIALSv3-12-1data collection
PHENIX1.19.2_4158refinement
Coot0.9.6.2-premodel building
Aimlessdata scaling
MOLREPphasing
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2A3L

2a3l


Resolution: 2.33→72.35 Å / SU ML: 0.3407 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.6919
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2675 6159 5.01 %
Rwork0.2368 116694 -
obs0.2383 122853 98.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.39 Å2
Refinement stepCycle: LAST / Resolution: 2.33→72.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20334 0 47 780 21161
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003920896
X-RAY DIFFRACTIONf_angle_d0.506428299
X-RAY DIFFRACTIONf_chiral_restr0.03953048
X-RAY DIFFRACTIONf_plane_restr0.00363658
X-RAY DIFFRACTIONf_dihedral_angle_d9.88077826
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.33-2.360.36921780.31173833X-RAY DIFFRACTION99.65
2.36-2.390.3462080.3083957X-RAY DIFFRACTION99.98
2.39-2.420.37971940.29373851X-RAY DIFFRACTION99.93
2.42-2.450.31451840.28023928X-RAY DIFFRACTION99.9
2.45-2.480.35262040.27983920X-RAY DIFFRACTION100
2.48-2.510.33052080.28623863X-RAY DIFFRACTION99.9
2.51-2.550.3142100.26133883X-RAY DIFFRACTION99.93
2.55-2.590.27761990.25633897X-RAY DIFFRACTION99.88
2.59-2.630.28932110.25183968X-RAY DIFFRACTION99.95
2.63-2.670.27072020.24673846X-RAY DIFFRACTION99.93
2.67-2.720.29012100.24943895X-RAY DIFFRACTION99.85
2.72-2.770.28082280.2593899X-RAY DIFFRACTION99.85
2.77-2.820.32132070.26043891X-RAY DIFFRACTION99.85
2.82-2.880.31231850.26593927X-RAY DIFFRACTION99.9
2.88-2.940.28492260.26713910X-RAY DIFFRACTION99.9
2.94-3.010.32452040.28033890X-RAY DIFFRACTION99.93
3.01-3.080.3031920.26233932X-RAY DIFFRACTION99.93
3.08-3.170.2782190.25443891X-RAY DIFFRACTION99.85
3.17-3.260.30721960.24713916X-RAY DIFFRACTION99.85
3.26-3.370.28582200.24173921X-RAY DIFFRACTION99.9
3.37-3.490.25092120.2333908X-RAY DIFFRACTION99.71
3.49-3.630.25641920.22973934X-RAY DIFFRACTION99.37
3.63-3.790.24292090.22613900X-RAY DIFFRACTION98.87
3.79-3.990.27741940.21733870X-RAY DIFFRACTION98.24
3.99-4.240.24282100.21493844X-RAY DIFFRACTION97.71
4.24-4.570.2251960.20373834X-RAY DIFFRACTION96.55
4.57-5.030.22722130.20023780X-RAY DIFFRACTION95.62
5.03-5.760.222070.21133847X-RAY DIFFRACTION95.93
5.76-7.250.25382070.23113851X-RAY DIFFRACTION95.57
7.25-72.350.23132340.21763908X-RAY DIFFRACTION94.42

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