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- PDB-2i6a: Human Adenosine Kinase in Complex With 5'-Deoxy-5-Iodotubercidin -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 2i6a
TitleHuman Adenosine Kinase in Complex With 5'-Deoxy-5-Iodotubercidin
ComponentsAdenosine kinase
KeywordsTRANSFERASE / protein-ligand complex / 5'-deoxy-5-iodotubercidin
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 / GMP salvage / Purine salvage / AMP salvage ...dATP biosynthetic process / adenosine kinase / adenosine kinase activity / ribonucleoside monophosphate biosynthetic process / dAMP salvage / deoxyadenosine kinase activity / Ribavirin ADME / GMP salvage / Purine salvage / AMP salvage / purine ribonucleoside salvage / purine nucleobase metabolic process / RNA binding / nucleoplasm / ATP binding / nucleus / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Adenosine kinase / Adenosine kinase, small domain - #10 / 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 / Adenosine kinase, small domain - #10 / 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-5I5 / Adenosine kinase / :
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.2 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 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

Deposited unit
A: Adenosine kinase
B: Adenosine kinase
C: Adenosine kinase
D: Adenosine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,5258
Polymers155,0214
Non-polymers1,5054
Water9,188510
1
A: Adenosine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1312
Polymers38,7551
Non-polymers3761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Adenosine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1312
Polymers38,7551
Non-polymers3761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Adenosine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1312
Polymers38,7551
Non-polymers3761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Adenosine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1312
Polymers38,7551
Non-polymers3761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.850, 66.930, 87.140
Angle α, β, γ (deg.)97.76, 103.70, 89.95
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Adenosine kinase / Adenylate kinase


Mass: 38755.219 Da / Num. of mol.: 4
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-5I5 / 7-(5-DEOXY-BETA-D-RIBOFURANOSYL)-5-IODO-7H-PYRROLO[2,3-D]PYRIMIDIN-4-AMINE / 5'-DEOXY-5-IODOTUBERCIDIN / (2R,3R,4S,5R)-2-(4-AMINO-5-IODO-7H-PYRROLO[2,3-D]PYRIMIDIN-7-YL)-5-(METHYL)TETRAHYDROFURAN-3,4-DIOL


Mass: 376.150 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H13IN4O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 510 / 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: 2.24 Å3/Da / Density % sol: 45.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: PEG 4000, 0.1 M MgCl2, pH 7.2, 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: 2.2→50 Å / Num. all: 41591 / Num. obs: 35353 / Observed criterion σ(I): 2

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Processing

Software
NameClassification
DMmodel building
BUSTERrefinement
HKL-2000data reduction
SCALEPACKdata scaling
DMphasing
RefinementMethod to determine structure: MIR / Resolution: 2.2→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.271 3516 -random
Rwork0.181 ---
all-41591 --
obs-35353 85.5 %-
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10828 0 76 510 11414

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