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1ake

STRUCTURE 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

Method: X-RAY DIFFRACTION Dmax: 91.0 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

ADENYLATE KINASE

Escherichia coli

UniProt P69441

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–214 Not recorded AP5 BIS(ADENOSINE)-5'-PENTAPHOSPHATE × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.00 Å
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 1–214 Not recorded AP5 BIS(ADENOSINE)-5'-PENTAPHOSPHATE × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.00 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 1AKE Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1E4V Mutant G10V of adenylate kinase from E. coli, modified in the Gly-loop Deposited 2000-07-12 Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–214（214 aa）
Mutation：G10V AP5 BIS(ADENOSINE)-5'-PENTAPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.7；pH 6.70
Resolution 1.85 Å
1E4V Mutant G10V of adenylate kinase from E. coli, modified in the Gly-loop Deposited 2000-07-12 Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–214（214 aa）
Mutation：G10V AP5 BIS(ADENOSINE)-5'-PENTAPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.7；pH 6.70
Resolution 1.85 Å
1E4Y Mutant P9L of adenylate kinase from E. coli, modified in the Gly-loop Deposited 2000-07-12 Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–214（214 aa）
Mutation：L9P AP5 BIS(ADENOSINE)-5'-PENTAPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.2；pH 7.20
Resolution 1.85 Å
1E4Y Mutant P9L of adenylate kinase from E. coli, modified in the Gly-loop Deposited 2000-07-12 Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–214（214 aa）
Mutation：L9P AP5 BIS(ADENOSINE)-5'-PENTAPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.2；pH 7.20
Resolution 1.85 Å
2ECK STRUCTURE OF PHOSPHOTRANSFERASE Deposited 1996-12-16 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–214（214 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.7；pH 6.7
Resolution 2.80 Å R-free 0.276
2ECK STRUCTURE OF PHOSPHOTRANSFERASE Deposited 1996-12-16 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–214（214 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.7；pH 6.7
Resolution 2.80 Å R-free 0.276
3HPQ Crystal structure of wild-type adenylate kinase from E. coli, in complex with Ap5A Deposited 2009-06-04 Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–214（214 aa）
Mutation：Wild-type AP5 BIS(ADENOSINE)-5'-PENTAPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；45 mg/ml AK in 50 mM MES pH 6.7, 1 mM EDTA, with 50% 50mM MES pH 7.0-7.3, 3% w/v PEG 2000 and 1.8-2.3 Ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.00 Å R-free 0.245
3HPQ Crystal structure of wild-type adenylate kinase from E. coli, in complex with Ap5A Deposited 2009-06-04 Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–214（214 aa）
Mutation：Wild-type AP5 BIS(ADENOSINE)-5'-PENTAPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；45 mg/ml AK in 50 mM MES pH 6.7, 1 mM EDTA, with 50% 50mM MES pH 7.0-7.3, 3% w/v PEG 2000 and 1.8-2.3 Ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.00 Å R-free 0.245
3HPR Crystal structure of V148G adenylate kinase from E. coli, in complex with Ap5A Deposited 2009-06-04 Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–214（214 aa）
Mutation：V148G AP5 BIS(ADENOSINE)-5'-PENTAPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；45 mg/ml AK in 50 mM MES pH 6.7, 1 mM EDTA, with 50% 50mM MES pH 7.0-7.3, 3% w/v PEG 2000 and 1.8-2.3 Ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.00 Å R-free 0.243
3HPR Crystal structure of V148G adenylate kinase from E. coli, in complex with Ap5A Deposited 2009-06-04 Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–214（214 aa）
Mutation：V148G AP5 BIS(ADENOSINE)-5'-PENTAPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；45 mg/ml AK in 50 mM MES pH 6.7, 1 mM EDTA, with 50% 50mM MES pH 7.0-7.3, 3% w/v PEG 2000 and 1.8-2.3 Ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.00 Å R-free 0.243
4AKE ADENYLATE KINASE Deposited 1995-12-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–214（214 aa）
Chain B 1–214（214 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.20 Å
4X8H Crystal structure of E. coli Adenylate kinase P177A mutant Deposited 2014-12-10 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–214（214 aa）
Mutation：P177A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；30% PEG 4K, 0.1 M Tris-HCl, 0.2 M MgCl2
Resolution 2.50 Å R-free 0.289
4X8L Crystal structure of E. coli Adenylate kinase P177A mutant in complex with inhibitor Ap5a Deposited 2014-12-10 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–214（214 aa）
Mutation：P177A AP5 BIS(ADENOSINE)-5'-PENTAPHOSPHATE × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；30% PEG 4K, 0.2 M AmAc, 0.1 M Tris-HCl, Ap5a in five time stoichiometric excess
Resolution 1.70 Å R-free 0.210
4X8L Crystal structure of E. coli Adenylate kinase P177A mutant in complex with inhibitor Ap5a Deposited 2014-12-10 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–214（214 aa）
Mutation：P177A AP5 BIS(ADENOSINE)-5'-PENTAPHOSPHATE × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；30% PEG 4K, 0.2 M AmAc, 0.1 M Tris-HCl, Ap5a in five time stoichiometric excess
Resolution 1.70 Å R-free 0.210
4X8M Crystal structure of E. coli Adenylate kinase Y171W mutant Deposited 2014-12-10 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: Monomeric
Chain A 1–214（214 aa）
Mutation：Y171W No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；28% PEG 4K, 0.2 M NaOAc, 0.1 M Tris-HCl
Resolution 2.60 Å R-free 0.309
4X8O Crystal structure of E. coli Adenylate kinase Y171W mutant in complex with inhibitor Ap5a Deposited 2014-12-10 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–214（214 aa）
Mutation：Y171W AP5 BIS(ADENOSINE)-5'-PENTAPHOSPHATE × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；28% PEG 4K, 0.1 M NaCit., 0.2 M AmAc
Resolution 2.10 Å R-free 0.239
4X8O Crystal structure of E. coli Adenylate kinase Y171W mutant in complex with inhibitor Ap5a Deposited 2014-12-10 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–214（214 aa）
Mutation：Y171W AP5 BIS(ADENOSINE)-5'-PENTAPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；28% PEG 4K, 0.1 M NaCit., 0.2 M AmAc
Resolution 2.10 Å R-free 0.239
6F7U Molecular Mechanism of ATP versus GTP Selectivity of Adenylate Kinase Deposited 2017-12-12 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–214（214 aa）
Not recorded GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；32% PEG 8000, 0.2 M Na-Acetate, 0.1 M Na-Cacodylate
Resolution 1.40 Å R-free 0.190
6HAM Adenylate kinase Deposited 2018-08-08 Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–214（214 aa）
Not recorded AP5 BIS(ADENOSINE)-5'-PENTAPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；292 K；14% PEG 4000 0.05M Tris pH=8
Resolution 2.55 Å R-free 0.243
7APU Structure of Adenylate kinase from Escherichia coli in complex with two ADP molecules refined at 1.36 A resolution. Deposited 2020-10-19 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–214（214 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 2 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；291.15 K；AdK at 18.3 mg/ml was mixed with 5 mM each of AMP and GTP in 30 mM MOPS buffer pH 7, containing 50 mM NaCl. Hanging drop: 2 ul of AdK, preincubated with AMP and GTP, and 2 ul of precipitant buffer containing 30% PEG 4000, 0.2 M NH4CH3CO2 (Ammonium Acetate), buffered with 100 mM CH3COONa (Sodium Acetate) adjusted to pH 4.6.
Resolution 1.36 Å R-free 0.206
7APU Structure of Adenylate kinase from Escherichia coli in complex with two ADP molecules refined at 1.36 A resolution. Deposited 2020-10-19 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–214（214 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 2 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；291.15 K；AdK at 18.3 mg/ml was mixed with 5 mM each of AMP and GTP in 30 mM MOPS buffer pH 7, containing 50 mM NaCl. Hanging drop: 2 ul of AdK, preincubated with AMP and GTP, and 2 ul of precipitant buffer containing 30% PEG 4000, 0.2 M NH4CH3CO2 (Ammonium Acetate), buffered with 100 mM CH3COONa (Sodium Acetate) adjusted to pH 4.6.
Resolution 1.36 Å R-free 0.206
8BQF Adenylate Kinase L107I MUTANT Deposited 2022-11-21 Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–214（214 aa）
Mutation：L107I AP5 BIS(ADENOSINE)-5'-PENTAPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；292 K；7.5% PEG 3,350, 7.5% PEG 4,000, 7.5% PEG 2,000, 7.5% PEG 5,000 monomethyl ether, 0.07M ammonium nitrate, 2.5% ethylene glycol and 0.05M MES pH=7.
Resolution 2.05 Å R-free 0.258
8BQF Adenylate Kinase L107I MUTANT Deposited 2022-11-21 Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–214（214 aa）
Mutation：L107I AP5 BIS(ADENOSINE)-5'-PENTAPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；292 K；7.5% PEG 3,350, 7.5% PEG 4,000, 7.5% PEG 2,000, 7.5% PEG 5,000 monomethyl ether, 0.07M ammonium nitrate, 2.5% ethylene glycol and 0.05M MES pH=7.
Resolution 2.05 Å R-free 0.258
8BQF Adenylate Kinase L107I MUTANT Deposited 2022-11-21 Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–214（214 aa）
Mutation：L107I AP5 BIS(ADENOSINE)-5'-PENTAPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；292 K；7.5% PEG 3,350, 7.5% PEG 4,000, 7.5% PEG 2,000, 7.5% PEG 5,000 monomethyl ether, 0.07M ammonium nitrate, 2.5% ethylene glycol and 0.05M MES pH=7.
Resolution 2.05 Å R-free 0.258
8BQF Adenylate Kinase L107I MUTANT Deposited 2022-11-21 Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 1–214（214 aa）
Mutation：L107I AP5 BIS(ADENOSINE)-5'-PENTAPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；292 K；7.5% PEG 3,350, 7.5% PEG 4,000, 7.5% PEG 2,000, 7.5% PEG 5,000 monomethyl ether, 0.07M ammonium nitrate, 2.5% ethylene glycol and 0.05M MES pH=7.
Resolution 2.05 Å R-free 0.258
8BQF Adenylate Kinase L107I MUTANT Deposited 2022-11-21 Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain E 1–214（214 aa）
Mutation：L107I AP5 BIS(ADENOSINE)-5'-PENTAPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；292 K；7.5% PEG 3,350, 7.5% PEG 4,000, 7.5% PEG 2,000, 7.5% PEG 5,000 monomethyl ether, 0.07M ammonium nitrate, 2.5% ethylene glycol and 0.05M MES pH=7.
Resolution 2.05 Å R-free 0.258
8BQF Adenylate Kinase L107I MUTANT Deposited 2022-11-21 Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain F 1–214（214 aa）
Mutation：L107I AP5 BIS(ADENOSINE)-5'-PENTAPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；292 K；7.5% PEG 3,350, 7.5% PEG 4,000, 7.5% PEG 2,000, 7.5% PEG 5,000 monomethyl ether, 0.07M ammonium nitrate, 2.5% ethylene glycol and 0.05M MES pH=7.
Resolution 2.05 Å R-free 0.258
8CRG E. coli adenylate kinase in complex with two ADP molecules as a result of enzymatic AP4A hydrolysis Deposited 2023-03-08 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–214（214 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 2 MPO 3[N-MORPHOLINO]PROPANE SULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291.15 K；20 % (w/v) PEG 3350, 100 mM Bis-tris propane pH 6.5
Resolution 1.49 Å R-free 0.191
8CRG E. coli adenylate kinase in complex with two ADP molecules as a result of enzymatic AP4A hydrolysis Deposited 2023-03-08 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–214（214 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291.15 K；20 % (w/v) PEG 3350, 100 mM Bis-tris propane pH 6.5
Resolution 1.49 Å R-free 0.191
8RJ4 E. coli adenylate kinase in complex with two ADP molecules and Mg2+ as a result of enzymatic AP4A hydrolysis Deposited 2023-12-20 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–214（214 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.4；291 K；24 % (w/v) PEG3350, 100 mM Bis-Tris propane pH 6.4
Resolution 2.11 Å R-free 0.253
8RJ4 E. coli adenylate kinase in complex with two ADP molecules and Mg2+ as a result of enzymatic AP4A hydrolysis Deposited 2023-12-20 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–214（214 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.4；291 K；24 % (w/v) PEG3350, 100 mM Bis-Tris propane pH 6.4
Resolution 2.11 Å R-free 0.253
8RJ4 E. coli adenylate kinase in complex with two ADP molecules and Mg2+ as a result of enzymatic AP4A hydrolysis Deposited 2023-12-20 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–214（214 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 2 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.4；291 K；24 % (w/v) PEG3350, 100 mM Bis-Tris propane pH 6.4
Resolution 2.11 Å R-free 0.253
8RJ4 E. coli adenylate kinase in complex with two ADP molecules and Mg2+ as a result of enzymatic AP4A hydrolysis Deposited 2023-12-20 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 1–214（214 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 2 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.4；291 K；24 % (w/v) PEG3350, 100 mM Bis-Tris propane pH 6.4
Resolution 2.11 Å R-free 0.253
8RJ6 E. coli adenylate kinase in complex with ATP and AMP and Mg2+ as a result of enzymatic AP4A hydrolysis. Deposited 2023-12-20 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–214（214 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 AMP ADENOSINE MONOPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；PEG3350, 100 mM Bis-Tris propane pH 7.0
Resolution 1.90 Å R-free 0.226
8RJ6 E. coli adenylate kinase in complex with ATP and AMP and Mg2+ as a result of enzymatic AP4A hydrolysis. Deposited 2023-12-20 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–214（214 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 AMP ADENOSINE MONOPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；PEG3350, 100 mM Bis-Tris propane pH 7.0
Resolution 1.90 Å R-free 0.226
8RJ9 E. coli adenylate kinase Asp84Ala variant in complex with two ADP molecules as a result of enzymatic AP4A hydrolysis. Deposited 2023-12-20 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–214（214 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；24-26% PEG3350, 100 mM Bis-Tris propane.
Resolution 1.59 Å R-free 0.203
8RJ9 E. coli adenylate kinase Asp84Ala variant in complex with two ADP molecules as a result of enzymatic AP4A hydrolysis. Deposited 2023-12-20 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–214（214 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；24-26% PEG3350, 100 mM Bis-Tris propane.
Resolution 1.59 Å R-free 0.203
9L14 Crystal structure of the monobody CL-1 in complex with the Escherichia coli adenylate kinase Deposited 2024-12-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–214（214 aa）
Not recorded AP5 BIS(ADENOSINE)-5'-PENTAPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1M HEPES buffer pH 7.5, 10% (v/v) 2-propanol, 20% (w/v) polyethylene glycol 4000
Resolution 1.86 Å R-free 0.235

19 other PDB entries and 38 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name KAD_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–214； UniProt 1–214 Author chain B； PDBConstruct 1–214； UniProt 1–214

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 1ake

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1ake
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1ake
Deposition date deposition_date1991-11-08
Structure title 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
Keywords keywordsTRANSFERASE(PHOSPHOTRANSFERASE); TRANSFERASE(PHOSPHOTRANSFERASE)
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier27.50 Å
Radius of gyration Rg (electron density) rg_electron27.17 Å
Forward intensity I(0) i043045600.00
Molecular weight molecular_weight48997.0 kDa
Excluded volume excluded_volume60609 ų
Envelope volume envelope_volume76279 ų
Hydration-shell volume shell_volume24103 ų
Envelope diameter envelope_diameter94.2 Å
Shell Rg shell_rg33.48 Å
Envelope Rg envelope_rg26.83 Å
Shape Rg shape_rg27.18 Å
Total Rg total_rg27.80 Å
Total atoms total_atoms3426
Residues n_residues428
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax91.0 Å
Rg (real space) rg_real27.64 Å
Rg uncertainty (real space) rg_real_error0.62 Å
I(0) (real space) i0_real4.3050e+07
I(0) uncertainty (real space) i0_real_error6.3640e+05
Rg (reciprocal space) rg_reciprocal27.60 Å
I(0) (reciprocal space) i0_reciprocal43040000.0000
Solution quality estimate total_estimate0.6808
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary23.5 Å
Skewness Skewness skewness0.345
Kurtosis Kurtosis kurtosis-0.729
Angular range angular_range— – 0.2900 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha9829000.0000
Real-space data points n_real_points59
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.747; Stabil: 1.000; Sysdev: 0.267; Positv: 1.000; Valcen: 0.818; Smooth: 0.987
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd1akea1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.1 — Nucleotide and nucleoside kinases
Domain ID domain_idd1akea2
Class classg — Small proteins
Fold Fold foldg.41 — Rubredoxin-like
Superfamily Superfamily superfamilyg.41.2 — Microbial and mitochondrial ADK, insert 'zinc finger' domain
Family Family familyg.41.2.1 — Microbial and mitochondrial ADK, insert 'zinc finger' domain
Domain ID domain_idd1akeb1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.1 — Nucleotide and nucleoside kinases
Domain ID domain_idd1akeb2
Class classg — Small proteins
Fold Fold foldg.41 — Rubredoxin-like
Superfamily Superfamily superfamilyg.41.2 — Microbial and mitochondrial ADK, insert 'zinc finger' domain
Family Family familyg.41.2.1 — Microbial and mitochondrial ADK, insert 'zinc finger' domain

CATH v4.4 (2 domains)

Domain ID domain_id1akeA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id1akeB00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
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8. Citations (3)

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9. Files and Curves (10)