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- PDB-4aql: HUMAN GUANINE DEAMINASE IN COMPLEX WITH VALACYCLOVIR -

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Basic information

Entry
Database: PDB / ID: 4aql
TitleHUMAN GUANINE DEAMINASE IN COMPLEX WITH VALACYCLOVIR
ComponentsGUANINE DEAMINASE
KeywordsHYDROLASE / PURINE METABOLISM
Function / homology
Function and homology information


guanine deaminase / guanine deaminase activity / guanine catabolic process / deoxyguanosine catabolic process / GMP catabolic process / : / dGMP catabolic process / guanine metabolic process / Purine catabolism / allantoin metabolic process ...guanine deaminase / guanine deaminase activity / guanine catabolic process / deoxyguanosine catabolic process / GMP catabolic process / : / dGMP catabolic process / guanine metabolic process / Purine catabolism / allantoin metabolic process / nucleobase-containing compound metabolic process / nervous system development / zinc ion binding / cytosol
Similarity search - Function
Guanine deaminase / : / Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / Roll ...Guanine deaminase / : / Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / Roll / TIM Barrel / Alpha-Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-TXC / Guanine deaminase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsWelin, M. / Egeblad, L. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Graslund, S. / Hammarstrom, M. ...Welin, M. / Egeblad, L. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Graslund, S. / Hammarstrom, M. / Johansson, I. / Karlberg, T. / Kotenyova, T. / Moche, M. / Nyman, T. / Persson, C. / Schuler, H. / Thorsell, A.G. / Tresaugues, L. / Weigelt, J. / Nordlund, P.
CitationJournal: Plos One / Year: 2012
Title: Pan-Pathway Based Interaction Profiling of Fda-Approved Nucleoside and Nucleobase Analogs with Enzymes of the Human Nucleotide Metabolism.
Authors: Egeblad, L. / Welin, M. / Flodin, S. / Graslund, S. / Wang, L. / Balzarini, J. / Eriksson, S. / Nordlund, P.
History
DepositionApr 18, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 2, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2012Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GUANINE DEAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0103
Polymers53,6211
Non-polymers3902
Water3,153175
1
A: GUANINE DEAMINASE
hetero molecules

A: GUANINE DEAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,0216
Polymers107,2412
Non-polymers7794
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545x,-y-1,-z1
Buried area4430 Å2
ΔGint-11.3 kcal/mol
Surface area31140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.729, 91.383, 131.913
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2137-

HOH

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Components

#1: Protein GUANINE DEAMINASE / GUANASE / GUANINE AMINASE / GUANINE AMINOHYDROLASE / GAH / P51-NEDASIN


Mass: 53620.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y2T3, guanine deaminase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-TXC / 2-[(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)methoxy]ethyl L-valinate / Valacyclovir


Mass: 324.336 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H20N6O4 / Comment: medication, antivirus*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.43 Å3/Da / Density % sol: 49.4 % / Description: NONE
Crystal growpH: 7 / Details: 20% PEG 6000 100 MM HEPES PH 7.0 200 MM MGCL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.918
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 14, 2010 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2→33 Å / Num. obs: 35909 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.4
Reflection shellResolution: 2→2.1 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 2.8 / % possible all: 96.7

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2UZ9

2uz9


Resolution: 1.99→65.96 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.939 / SU B: 3.477 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21375 1793 5 %RANDOM
Rwork0.1805 ---
obs0.18222 34084 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.937 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.24 Å2
Refinement stepCycle: LAST / Resolution: 1.99→65.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3505 0 24 175 3704
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.023611
X-RAY DIFFRACTIONr_bond_other_d0.0010.022421
X-RAY DIFFRACTIONr_angle_refined_deg1.4541.9614887
X-RAY DIFFRACTIONr_angle_other_deg0.9213.0015895
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8685443
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.1824.32169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.84915623
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2711518
X-RAY DIFFRACTIONr_chiral_restr0.0910.2546
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024014
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02745
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.994→2.046 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 107 -
Rwork0.309 2215 -
obs--92.88 %

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