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- PDB-2i6b: Human Adenosine Kinase in Complex with An Acetylinic Inhibitor -

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Basic information

Entry
Database: PDB / ID: 2i6b
TitleHuman Adenosine Kinase in Complex with An Acetylinic Inhibitor
ComponentsAdenosine kinase
KeywordsTRANSFERASE / Protein-ligand complex
Function / homology
Function and homology information


dATP biosynthetic process / adenosine kinase / adenosine kinase activity / ribonucleoside monophosphate biosynthetic process / dAMP salvage / deoxyadenosine kinase activity / Ribavirin ADME / Purine salvage / GMP salvage / AMP salvage ...dATP biosynthetic process / adenosine kinase / adenosine kinase activity / ribonucleoside monophosphate biosynthetic process / dAMP salvage / deoxyadenosine kinase activity / Ribavirin ADME / Purine salvage / GMP salvage / AMP salvage / purine ribonucleoside salvage / purine nucleobase metabolic process / RNA binding / nucleoplasm / ATP binding / metal ion binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Adenosine kinase, small domain - #10 / Adenosine kinase / Adenosine kinase, small domain / pfkB family of carbohydrate kinases signature 2. / Carbohydrate/purine kinase, PfkB, conserved site / Carbohydrate kinase PfkB / pfkB family carbohydrate kinase / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase ...Adenosine kinase, small domain - #10 / Adenosine kinase / Adenosine kinase, small domain / pfkB family of carbohydrate kinases signature 2. / Carbohydrate/purine kinase, PfkB, conserved site / Carbohydrate kinase PfkB / pfkB family carbohydrate kinase / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-89I / Adenosine kinase / :
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMuchmore, S.W.
CitationJournal: J.Med.Chem. / Year: 2006
Title: Crystal structures of human adenosine kinase inhibitor complexes reveal two distinct binding modes.
Authors: Muchmore, S.W. / Smith, R.A. / Stewart, A.O. / Cowart, M.D. / Gomtsyan, A. / Matulenko, M.A. / Yu, H. / Severin, J.M. / Bhagwat, S.S. / Lee, C.H. / Kowaluk, E.A. / Jarvis, M.F. / Jakob, C.L.
History
DepositionAug 28, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 2, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Aug 30, 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 / 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 / _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: Adenosine kinase
B: Adenosine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,3114
Polymers77,5102
Non-polymers8012
Water4,252236
1
A: Adenosine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1562
Polymers38,7551
Non-polymers4001
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Adenosine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1562
Polymers38,7551
Non-polymers4001
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.180, 58.200, 89.210
Angle α, β, γ (deg.)90.00, 107.54, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Adenosine kinase / Adenylate kinase


Mass: 38755.219 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADK / Production host: Escherichia coli (E. coli) / References: UniProt: Q5VXR3, UniProt: P55263*PLUS
#2: Chemical ChemComp-89I / 5-[4-(DIMETHYLAMINO)PHENYL]-6-[(6-MORPHOLIN-4-YLPYRIDIN-3-YL)ETHYNYL]PYRIMIDIN-4-AMINE


Mass: 400.476 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H24N6O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 2.27 Å3/Da / Density % sol: 45.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: PEG4000, 0.1 M MgCl2, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
RadiationMonochromator: Silicon 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 31045 / Num. obs: 25799 / % possible obs: 87.5 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.068

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Processing

Software
NameClassification
AMoREphasing
BUSTERrefinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 2I6A

2i6a


Resolution: 2.3→50 Å / Cross valid method: THROUGHOUT / σ(F): 4 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.291 1378 -Random
Rwork0.221 ---
all-31045 --
obs-25799 87.5 %-
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5151 0 60 236 5447

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