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- PDB-1ake: STRUCTURE OF THE COMPLEX BETWEEN ADENYLATE KINASE FROM ESCHERICHI... -

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Entry
Database: PDB / ID: 1ake
TitleSTRUCTURE OF THE COMPLEX BETWEEN ADENYLATE KINASE FROM ESCHERICHIA COLI AND THE INHIBITOR AP5A REFINED AT 1.9 ANGSTROMS RESOLUTION: A MODEL FOR A CATALYTIC TRANSITION STATE
ComponentsADENYLATE KINASE
KeywordsTRANSFERASE(PHOSPHOTRANSFERASE)
Function / homology
Function and homology information


purine ribonucleotide interconversion / adenine metabolic process / nucleoside monophosphate metabolic process / ADP biosynthetic process / nucleoside diphosphate metabolic process / adenylate kinase / AMP kinase activity / AMP salvage / nucleoside diphosphate kinase activity / AMP binding ...purine ribonucleotide interconversion / adenine metabolic process / nucleoside monophosphate metabolic process / ADP biosynthetic process / nucleoside diphosphate metabolic process / adenylate kinase / AMP kinase activity / AMP salvage / nucleoside diphosphate kinase activity / AMP binding / magnesium ion binding / ATP binding / cytosol / cytoplasm
Similarity search - Function
Adenylate kinase, active site lid domain / Adenylate kinase, active site lid / Adenylate kinase subfamily / Adenylate kinase, conserved site / Adenylate kinase signature. / Adenylate kinase/UMP-CMP kinase / Adenylate kinase / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase ...Adenylate kinase, active site lid domain / Adenylate kinase, active site lid / Adenylate kinase subfamily / Adenylate kinase, conserved site / Adenylate kinase signature. / Adenylate kinase/UMP-CMP kinase / Adenylate kinase / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BIS(ADENOSINE)-5'-PENTAPHOSPHATE / Adenylate kinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsMueller, C.W. / Schulz, G.E.
Citation
Journal: J.Mol.Biol. / Year: 1992
Title: Structure of the complex between adenylate kinase from Escherichia coli and the inhibitor Ap5A refined at 1.9 A resolution. A model for a catalytic transition state.
Authors: Muller, C.W. / Schulz, G.E.
#1: Journal: J.Mol.Biol. / Year: 1990
Title: Induced-Fit Movements in Adenylate Kinases
Authors: Schulz, G.E. / Mueller, C.W. / Diederichs, K.
#2: Journal: J.Mol.Biol. / Year: 1988
Title: Structure of the Complex of Adenylate Kinase from Escherichia Coli with the Inhibitor P1, P5-Bis (Adenosine-5'-) Pentaphosphate
Authors: Mueller, C.W. / Schulz, G.E.
History
DepositionNov 8, 1991Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_distant_solvent_atoms / pdbx_entry_details ...pdbx_distant_solvent_atoms / pdbx_entry_details / pdbx_validate_close_contact / struct_conn

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ADENYLATE KINASE
B: ADENYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0734
Polymers47,2402
Non-polymers1,8332
Water6,810378
1
A: ADENYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5362
Polymers23,6201
Non-polymers9161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ADENYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5362
Polymers23,6201
Non-polymers9161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.200, 79.800, 85.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221
Atom site foot note1: CIS PROLINE - PRO A 87 / 2: CIS PROLINE - PRO B 87
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.995341, 0.068333, 0.068023), (0.038108, 0.92686, -0.373469), (-0.088568, -0.369136, -0.925145)
Vector: 38.70362, 47.46029, 42.28705)
DetailsTHE TRANSFORMATION PRESENTED ON THE *MTRIX* RECORDS WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *A* WHEN APPLIED TO CHAIN *B*.

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Components

#1: Protein ADENYLATE KINASE


Mass: 23620.029 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P69441, adenylate kinase
#2: Chemical ChemComp-AP5 / BIS(ADENOSINE)-5'-PENTAPHOSPHATE


Mass: 916.367 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H29N10O22P5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 378 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.17 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 6.7 / Method: vapor diffusion, hanging drop / Details: referred to J.Mol.Biol. 202.909-912 1988
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120-25 mg/mlprotein1drop
22 mMAp5A1drop
350 mMMES1drop
41.5 %(w/v)PEG15001drop
51.5 Mammonium sulfate1drop
650 mMMES1reservoir
72.0-2.2 Mammonium sulfate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.85 Å / Lowest resolution: 9999 Å / Num. obs: 40700 / % possible obs: 94.1 % / Num. measured all: 156159 / Rmerge(I) obs: 0.147
Reflection shell
*PLUS
Highest resolution: 1.85 Å / Lowest resolution: 1.98 Å / % possible obs: 92.8 % / Num. unique obs: 7170 / Rmerge(I) obs: 0.805

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2→10 Å / Rfactor Rwork: 0.196 / Rfactor obs: 0.196 / σ(F): 0
Details: IN COMPLEX-I ARG 167 AND PHOSPHATE-4 OF AP5 ADOPT TWO CONFORMATIONS. BOTH CONFORMATIONS WERE REFINED ALTERNATINGLY. NOTE THAT THE DISTANCE PD - O3D FOR CONFORMATION A OF AP5 A 215 IS 2.13 ...Details: IN COMPLEX-I ARG 167 AND PHOSPHATE-4 OF AP5 ADOPT TWO CONFORMATIONS. BOTH CONFORMATIONS WERE REFINED ALTERNATINGLY. NOTE THAT THE DISTANCE PD - O3D FOR CONFORMATION A OF AP5 A 215 IS 2.13 ANGSTROMS WHICH IS LARGER THAN EXPECTED. NOTE FURTHER THAT CONFORMATION A OF THIS ENTRY CORRESPONDS TO CONFORMATION A' OF THE PAPER CITED ON JRNL RECORDS ABOVE AND CONFORMATION B CORRESPONDS TO CONFORMATION B' OF THE PUBLICATION.
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3317 0 121 378 3816
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 10 Å / σ(F): 0 / Rfactor all: 0.196
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3.2

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