3hpq

Crystal structure of wild-type adenylate kinase from E. coli, in complex with Ap5A

Method: X-RAY DIFFRACTION D_max: 81.8 Å Quality: REASONABLE

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Adenylate kinase

Escherichia coli

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	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
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–214	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

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 3HPQ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
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 Deposited 1991-11-08	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）	Not recorded	AP5 BIS(ADENOSINE)-5'-PENTAPHOSPHATE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å
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 Deposited 1991-11-08	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）	Not recorded	AP5 BIS(ADENOSINE)-5'-PENTAPHOSPHATE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 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 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 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）	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 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）	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
3HPR Crystal structure of V148G adenylate kinase from E. coli, in complex with Ap5A Deposited 2009-06-04	Different mutation/modification 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 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 experimental conditions 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 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）	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 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）	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 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）	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 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）	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 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）	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 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）	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 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）	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 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）	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 mutation/modification 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 mutation/modification 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 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）	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 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）	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 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）	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 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）	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 mutation/modification 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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3hpq
Deposition date deposition_date	2009-06-04
Structure title title	Crystal structure of wild-type adenylate kinase from E. coli, in complex with Ap5A
Keywords keywords	Enzyme Inhibitor Complex, ATP-binding, Kinase, Nucleotide biosynthesis, Nucleotide-binding, Transferase; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	25.98 Å
Radius of gyration Rg (electron density) rg_electron	25.44 Å
Forward intensity I(0) i0	43203700.00
Molecular weight molecular_weight	48997.0 kDa
Excluded volume excluded_volume	60609 Å³
Envelope volume envelope_volume	75023 Å³
Hydration-shell volume shell_volume	24919 Å³
Envelope diameter envelope_diameter	84.5 Å
Shell Rg shell_rg	32.23 Å
Envelope Rg envelope_rg	25.28 Å
Shape Rg shape_rg	25.44 Å
Total Rg total_rg	26.17 Å
Total atoms total_atoms	3426
Residues n_residues	428
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	81.8 Å
Rg (real space) rg_real	26.04 Å
Rg uncertainty (real space) rg_real_error	0.52 Å
I(0) (real space) i0_real	4.3200e+07
I(0) uncertainty (real space) i0_real_error	6.2110e+05
Rg (reciprocal space) rg_reciprocal	26.02 Å
I(0) (reciprocal space) i0_reciprocal	43200000.0000
Solution quality estimate total_estimate	0.7159
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.5 Å
Skewness Skewness skewness	0.338
Kurtosis Kurtosis kurtosis	-0.624
Angular range angular_range	— – 0.3050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8268000.0000
Real-space data points n_real_points	62
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.911; Stabil: 1.000; Sysdev: 0.221; Positv: 1.000; Valcen: 0.943; Smooth: 0.966

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Adenylate kinase
Molecular weight formula_weight	23620.0 kDa
EC 编号 ec_number	2.7.4.3
Mutation mutation	Wild-type
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4098

MRIILLGAPGAGKGTQAQFIMEKYGIPQISTGDMLRAAVKSGSELGKQAKDIMDAGKLVTDELVIALVKERIAQEDCRNGFLLDGFPRTIPQADAMKEAGINVDYVLEFDVPDELIVDRIVGRRVHAPSGRVYHVKFNPPKVEGKDDVTGEELTTRKDDQEETVRKRLVEYHQMTAPLIGYYSKEAEAGNTKYAKVDGTKPVAEVRADLEKILG

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	83333
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	BIS(ADENOSINE)-5'-PENTAPHOSPHATE
Molecular weight formula_weight	916.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	661

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3hpqa1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.1 — Nucleotide and nucleoside kinases

Domain ID domain_id	d3hpqa2
Class class	g — Small proteins
Fold Fold fold	g.41 — Rubredoxin-like
Superfamily Superfamily superfamily	g.41.2 — Microbial and mitochondrial ADK, insert 'zinc finger' domain
Family Family family	g.41.2.1 — Microbial and mitochondrial ADK, insert 'zinc finger' domain

Domain ID domain_id	d3hpqb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.1 — Nucleotide and nucleoside kinases

Domain ID domain_id	d3hpqb2
Class class	g — Small proteins
Fold Fold fold	g.41 — Rubredoxin-like
Superfamily Superfamily superfamily	g.41.2 — Microbial and mitochondrial ADK, insert 'zinc finger' domain
Family Family family	g.41.2.1 — Microbial and mitochondrial ADK, insert 'zinc finger' domain

CATH v4.4 (2 domains)

Domain ID domain_id	3hpqA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	3hpqB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

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8. Citations (1)

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Unit-cell length a length_a	83.646 Å
Unit-cell length b length_b	72.639 Å
Unit-cell length c length_c	78.699 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	14.999 Å
R factor r_factor	0.2040
R_work r_work	0.1994
R_free r_free	0.2454

fit	/app/data/saxs_computation/hp/3hpq/3hpq.fit
pddf	/app/data/pr_computation/hp/3hpq/3hpq.pr.out
profile	/app/data/saxs_computation/hp/3hpq/3hpq.dat