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3jzi

Crystal structure of biotin carboxylase from E. Coli in complex with benzimidazole series

Method: X-RAY DIFFRACTION Dmax: 113.9 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Biotin carboxylase

Escherichia coli

UniProt P24182

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1–449 Chain B； UniProt 1–449 Not recorded JZL 7-amino-2-[(2-chlorobenzyl)amino]-1-{[(1S,2S)-2-hydroxycycloheptyl]methyl}-1H-benzimidazole-5-carboxamide × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8；295 K；Co-crystallization. 8-10% PEG6000, 100mM Tris-HCl., VAPOR DIFFUSION, SITTING DROP, temperature 295K Resolution 2.31 Å R-free 0.223

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 3JZI Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1BNC THREE-DIMENSIONAL STRUCTURE OF THE BIOTIN CARBOXYLASE SUBUNIT OF ACETYL-COA CARBOXYLASE Deposited 1994-07-06 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–449（449 aa）
Chain B 1–449（449 aa）
Not recorded PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.40 Å
1DV1 STRUCTURE OF BIOTIN CARBOXYLASE (APO) Deposited 2000-01-19 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–449（449 aa）
Chain B 1–449（449 aa）
Not recorded PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions MICRODIALYSIS；pH 7；298 K；10mM potassium phosphate 1mM EDTA 2mM DTT, pH 7.0, MICRODIALYSIS, temperature 298.0K
Resolution 1.90 Å R-free 0.238
1DV2 The structure of biotin carboxylase, mutant E288K, complexed with ATP Deposited 2000-01-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–449（449 aa） Fragment：BIOTIN CARBOXYLASE
Mutation：E288K ATP ADENOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；PEG-8000 ATP magnesium chloride HEPPS potassium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.50 Å R-free 0.203
1DV2 The structure of biotin carboxylase, mutant E288K, complexed with ATP Deposited 2000-01-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–449（449 aa） Fragment：BIOTIN CARBOXYLASE
Mutation：E288K ATP ADENOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；PEG-8000 ATP magnesium chloride HEPPS potassium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.50 Å R-free 0.203
2GPS Crystal Structure of the Biotin Carboxylase Subunit, E23R mutant, of Acetyl-CoA Carboxylase from Escherichia coli. Deposited 2006-04-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–449（449 aa）
Mutation：E23R No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；294 K；0.1 M magnesium formate, 14% (w/v) PEG3350, 8% (v/v) glycerol, and 20 mM calcium chloride, pH 8.5, VAPOR DIFFUSION, temperature 294K
Resolution 2.80 Å R-free 0.260
2GPS Crystal Structure of the Biotin Carboxylase Subunit, E23R mutant, of Acetyl-CoA Carboxylase from Escherichia coli. Deposited 2006-04-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–449（449 aa）
Mutation：E23R No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；294 K；0.1 M magnesium formate, 14% (w/v) PEG3350, 8% (v/v) glycerol, and 20 mM calcium chloride, pH 8.5, VAPOR DIFFUSION, temperature 294K
Resolution 2.80 Å R-free 0.260
2GPW Crystal Structure of the Biotin Carboxylase Subunit, F363A Mutant, of Acetyl-CoA Carboxylase from Escherichia coli. Deposited 2006-04-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–449（449 aa）
Mutation：F363A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；294 K；0.1 M Bis-Tris (pH 7.5), 100 mM NaCl, 200 mM trimethylamine N-oxide, 8% (v/v) PEG2000 MME, 4% (v/v) glycerol, 5 mM magnesium chloride, and 2.5 mM DTT, VAPOR DIFFUSION, temperature 294K
Resolution 2.20 Å R-free 0.250
2GPW Crystal Structure of the Biotin Carboxylase Subunit, F363A Mutant, of Acetyl-CoA Carboxylase from Escherichia coli. Deposited 2006-04-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–449（449 aa）
Mutation：F363A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；294 K；0.1 M Bis-Tris (pH 7.5), 100 mM NaCl, 200 mM trimethylamine N-oxide, 8% (v/v) PEG2000 MME, 4% (v/v) glycerol, 5 mM magnesium chloride, and 2.5 mM DTT, VAPOR DIFFUSION, temperature 294K
Resolution 2.20 Å R-free 0.250
2GPW Crystal Structure of the Biotin Carboxylase Subunit, F363A Mutant, of Acetyl-CoA Carboxylase from Escherichia coli. Deposited 2006-04-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–449（449 aa）
Mutation：F363A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；294 K；0.1 M Bis-Tris (pH 7.5), 100 mM NaCl, 200 mM trimethylamine N-oxide, 8% (v/v) PEG2000 MME, 4% (v/v) glycerol, 5 mM magnesium chloride, and 2.5 mM DTT, VAPOR DIFFUSION, temperature 294K
Resolution 2.20 Å R-free 0.250
2GPW Crystal Structure of the Biotin Carboxylase Subunit, F363A Mutant, of Acetyl-CoA Carboxylase from Escherichia coli. Deposited 2006-04-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 1–449（449 aa）
Mutation：F363A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；294 K；0.1 M Bis-Tris (pH 7.5), 100 mM NaCl, 200 mM trimethylamine N-oxide, 8% (v/v) PEG2000 MME, 4% (v/v) glycerol, 5 mM magnesium chloride, and 2.5 mM DTT, VAPOR DIFFUSION, temperature 294K
Resolution 2.20 Å R-free 0.250
2J9G Crystal structure of Biotin carboxylase from E. coli in complex with AMPPNP and ADP Deposited 2008-03-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–449（449 aa）
Not recorded MG MAGNESIUM ION × 1 SO4 SULFATE ION × 1 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 0.1M BIS-TRIS PH 6.5, 0.2M CACL2, 45% MPD
Resolution 2.05 Å R-free 0.236
2J9G Crystal structure of Biotin carboxylase from E. coli in complex with AMPPNP and ADP Deposited 2008-03-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–449（449 aa）
Not recorded MG MAGNESIUM ION × 1 SO4 SULFATE ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 0.1M BIS-TRIS PH 6.5, 0.2M CACL2, 45% MPD
Resolution 2.05 Å R-free 0.236
2V58 CRYSTAL STRUCTURE OF BIOTIN CARBOXYLASE FROM E.COLI IN COMPLEX WITH POTENT INHIBITOR 1 Deposited 2008-10-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–449（449 aa）
Not recorded LZJ 6-(2,6-dibromophenyl)pyrido[2,3-d]pyrimidine-2,7-diamine × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions PROTEIN: 12 MG/ML, (250 MM POTASSIUM CHLORIDE, 10 MM HEPES, PH 7.2) WELL: 0.1 M POTASSIUM CHLORIDE AND 4% (W/V) PEG 8000
Resolution 2.10 Å R-free 0.219
2V58 CRYSTAL STRUCTURE OF BIOTIN CARBOXYLASE FROM E.COLI IN COMPLEX WITH POTENT INHIBITOR 1 Deposited 2008-10-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–449（449 aa）
Not recorded LZJ 6-(2,6-dibromophenyl)pyrido[2,3-d]pyrimidine-2,7-diamine × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions PROTEIN: 12 MG/ML, (250 MM POTASSIUM CHLORIDE, 10 MM HEPES, PH 7.2) WELL: 0.1 M POTASSIUM CHLORIDE AND 4% (W/V) PEG 8000
Resolution 2.10 Å R-free 0.219
2V59 CRYSTAL STRUCTURE OF BIOTIN CARBOXYLASE FROM E.COLI IN COMPLEX WITH POTENT INHIBITOR 2 Deposited 2008-10-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–449（449 aa）
Not recorded LZK 6-(2,6-DIMETHOXYPHENYL)PYRIDO[2,3-D]PYRIMIDINE-2,7-DIAMINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions WELL: 0.1 M POTASSIUM CHLORIDE, 4% (W/V) PEG 8000 PROTEIN: 12 MG/ML, 250 MM POTASSIUM CHLORIDE, 10 MM HEPES, PH 7.2
Resolution 2.40 Å R-free 0.248
2V59 CRYSTAL STRUCTURE OF BIOTIN CARBOXYLASE FROM E.COLI IN COMPLEX WITH POTENT INHIBITOR 2 Deposited 2008-10-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–449（449 aa）
Not recorded LZK 6-(2,6-DIMETHOXYPHENYL)PYRIDO[2,3-D]PYRIMIDINE-2,7-DIAMINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions WELL: 0.1 M POTASSIUM CHLORIDE, 4% (W/V) PEG 8000 PROTEIN: 12 MG/ML, 250 MM POTASSIUM CHLORIDE, 10 MM HEPES, PH 7.2
Resolution 2.40 Å R-free 0.248
2V5A CRYSTAL STRUCTURE OF BIOTIN CARBOXYLASE FROM E.COLI IN COMPLEX WITH POTENT INHIBITOR 3 Deposited 2008-10-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–449（449 aa）
Not recorded LZL 7-(2,5-dihydropyrrol-1-yl)-6-phenyl-pyrido[6,5-d]pyrimidin-2-amine × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 0.1 M POTASSIUM CHLORIDE, 4% (W/V) PEG 8000
Resolution 2.31 Å R-free 0.237
2V5A CRYSTAL STRUCTURE OF BIOTIN CARBOXYLASE FROM E.COLI IN COMPLEX WITH POTENT INHIBITOR 3 Deposited 2008-10-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–449（449 aa）
Not recorded CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 0.1 M POTASSIUM CHLORIDE, 4% (W/V) PEG 8000
Resolution 2.31 Å R-free 0.237
2VR1 Crystal structure of Biotin carboxylase from E. coli in complex with ATP analog, ADPCF2P. Deposited 2008-03-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–449（449 aa）
Not recorded CL CHLORIDE ION × 1 ATF PHOSPHODIFLUOROMETHYLPHOSPHONIC ACID-ADENYLATE ESTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 0.1M KCL, 3-8% PEG 8000
Resolution 2.60 Å R-free 0.247
2VR1 Crystal structure of Biotin carboxylase from E. coli in complex with ATP analog, ADPCF2P. Deposited 2008-03-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–449（449 aa）
Not recorded CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 0.1M KCL, 3-8% PEG 8000
Resolution 2.60 Å R-free 0.247
2W6M Crystal structure of Biotin carboxylase from E. coli in complex with amino-oxazole fragment series Deposited 2008-12-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–449（449 aa）
Not recorded OA1 (2-AMINO-1,3-OXAZOL-5-YL)-(3-BROMOPHENYL)METHANONE × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.00 Å R-free 0.208
2W6M Crystal structure of Biotin carboxylase from E. coli in complex with amino-oxazole fragment series Deposited 2008-12-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–449（449 aa）
Not recorded OA1 (2-AMINO-1,3-OXAZOL-5-YL)-(3-BROMOPHENYL)METHANONE × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.00 Å R-free 0.208
2W6N Crystal structure of Biotin carboxylase from E. coli in complex with amino-oxazole fragment series Deposited 2008-12-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–449（449 aa）
Not recorded OA2 2-AMINO-N,N-BIS(PHENYLMETHYL)-1,3-OXAZOLE-5-CARBOXAMIDE × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 0.1 M KCL AND 2-8% PEG-800
Resolution 1.87 Å R-free 0.217
2W6N Crystal structure of Biotin carboxylase from E. coli in complex with amino-oxazole fragment series Deposited 2008-12-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–449（449 aa）
Not recorded OA2 2-AMINO-N,N-BIS(PHENYLMETHYL)-1,3-OXAZOLE-5-CARBOXAMIDE × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 0.1 M KCL AND 2-8% PEG-800
Resolution 1.87 Å R-free 0.217
2W6O Crystal structure of Biotin carboxylase from E. coli in complex with 4-Amino-7,7-dimethyl-7,8-dihydro-quinazolinone fragment Deposited 2008-12-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–449（449 aa）
Not recorded OA3 4-amino-7,7-dimethyl-7,8-dihydroquinazolin-5(6H)-one × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.50 Å R-free 0.308
2W6O Crystal structure of Biotin carboxylase from E. coli in complex with 4-Amino-7,7-dimethyl-7,8-dihydro-quinazolinone fragment Deposited 2008-12-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–449（449 aa）
Not recorded OA3 4-amino-7,7-dimethyl-7,8-dihydroquinazolin-5(6H)-one × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.50 Å R-free 0.308
2W6P Crystal structure of Biotin carboxylase from E. coli in complex with 5-Methyl-6-phenyl-quinazoline-2,4-diamine Deposited 2008-12-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–449（449 aa）
Not recorded OA4 5-methyl-6-phenylquinazoline-2,4-diamine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 0.1 M KCL AND 2-8% PEG-800
Resolution 1.85 Å R-free 0.216
2W6P Crystal structure of Biotin carboxylase from E. coli in complex with 5-Methyl-6-phenyl-quinazoline-2,4-diamine Deposited 2008-12-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–449（449 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions 0.1 M KCL AND 2-8% PEG-800
Resolution 1.85 Å R-free 0.216
2W6Q Crystal structure of Biotin carboxylase from E. coli in complex with the triazine-2,4-diamine fragment Deposited 2008-12-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–449（449 aa）
Not recorded OA5 6-(2-phenoxyethoxy)-1,3,5-triazine-2,4-diamine × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 0.1M KCL AND 2-8% PEG-800
Resolution 2.05 Å R-free 0.224
2W6Q Crystal structure of Biotin carboxylase from E. coli in complex with the triazine-2,4-diamine fragment Deposited 2008-12-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–449（449 aa）
Not recorded OA5 6-(2-phenoxyethoxy)-1,3,5-triazine-2,4-diamine × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 0.1M KCL AND 2-8% PEG-800
Resolution 2.05 Å R-free 0.224
2W6Z Crystal structure of Biotin carboxylase from E. coli in complex with the 3-(3-Methyl-but-2-enyl)-3H-purin-6-ylamine fragment Deposited 2008-12-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–449（449 aa）
Not recorded L21 3-(3-methylbut-2-en-1-yl)-3H-purin-6-amine × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 0.1M KCL AND 2-8% PEG 800
Resolution 1.90 Å R-free 0.220
2W6Z Crystal structure of Biotin carboxylase from E. coli in complex with the 3-(3-Methyl-but-2-enyl)-3H-purin-6-ylamine fragment Deposited 2008-12-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–449（449 aa）
Not recorded CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 0.1M KCL AND 2-8% PEG 800
Resolution 1.90 Å R-free 0.220
2W70 Crystal structure of Biotin carboxylase from E. coli in complex with the amino-thiazole-pyrimidine fragment Deposited 2008-12-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–449（449 aa）
Not recorded L22 4-(2-amino-1,3-thiazol-4-yl)pyrimidin-2-amine × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.77 Å R-free 0.202
2W70 Crystal structure of Biotin carboxylase from E. coli in complex with the amino-thiazole-pyrimidine fragment Deposited 2008-12-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–449（449 aa）
Not recorded L22 4-(2-amino-1,3-thiazol-4-yl)pyrimidin-2-amine × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.77 Å R-free 0.202
2W71 Crystal structure of Biotin carboxylase from E. coli in complex with the imidazole-pyrimidine inhibitor Deposited 2008-12-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–449（449 aa）
Not recorded CL CHLORIDE ION × 1 L23 4-[1-(2,6-dichlorobenzyl)-2-methyl-1H-imidazol-4-yl]pyrimidin-2-amine × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.99 Å R-free 0.229
2W71 Crystal structure of Biotin carboxylase from E. coli in complex with the imidazole-pyrimidine inhibitor Deposited 2008-12-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–449（449 aa）
Not recorded CL CHLORIDE ION × 1 L23 4-[1-(2,6-dichlorobenzyl)-2-methyl-1H-imidazol-4-yl]pyrimidin-2-amine × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.99 Å R-free 0.229
3G8C Crystal Structure of Biotin Carboxylase in Complex with Biotin, Bicarbonate, ADP and Mg Ion Deposited 2009-02-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–444（444 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 BTN BIOTIN × 1 BCT BICARBONATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；23% PEG3350, 0.12M Li2SO4, 3.9% SORBITOL, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.00 Å R-free 0.216
3G8C Crystal Structure of Biotin Carboxylase in Complex with Biotin, Bicarbonate, ADP and Mg Ion Deposited 2009-02-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–444（444 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 BTN BIOTIN × 1 BCT BICARBONATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；23% PEG3350, 0.12M Li2SO4, 3.9% SORBITOL, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.00 Å R-free 0.216
3G8D Crystal structure of the biotin carboxylase subunit, E296A mutant, of acetyl-COA carboxylase from Escherichia coli Deposited 2009-02-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–444（444 aa）
Mutation：E296A SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；23% PEG3350, 0.12M Li2SO4, 3.9% SORBITOL, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 1.90 Å R-free 0.226
3G8D Crystal structure of the biotin carboxylase subunit, E296A mutant, of acetyl-COA carboxylase from Escherichia coli Deposited 2009-02-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–444（444 aa）
Mutation：E296A SO4 SULFATE ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；23% PEG3350, 0.12M Li2SO4, 3.9% SORBITOL, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 1.90 Å R-free 0.226
3JZF Crystal structure of biotin carboxylase from E. Coli in complex with benzimidazoles series Deposited 2009-09-23 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–449（449 aa）
Chain B 1–449（449 aa）
Not recorded CO3 CARBONATE ION × 1 JZK 2-[(2-chlorobenzyl)amino]-1-(cyclohexylmethyl)-1H-benzimidazole-5-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；295 K；Co-crystallzation. 8-10% PEG 6000, Tris-HCl pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 2.13 Å R-free 0.236
3RUP Crystal structure of E.coli biotin carboxylase in complex with two ADP and two Ca ions Deposited 2011-05-05 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–449（449 aa）
Chain B 1–449（449 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 4 CA CALCIUM ION × 4 CL CHLORIDE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；PEG3350, CaCl2, pH 8.5, vapor diffusion, sitting drop, temperature 295K
Resolution 1.99 Å R-free 0.227
3RV3 Crystal structure of E.coli biotin carboxylase in complex with two ADP and one Mg ion Deposited 2011-05-05 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–449（449 aa）
Chain B 1–449（449 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 4 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.2；295 K；Bis-Tris, PEG3350, NH4Cl, n-octyl-beta-D-glucose, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 1.91 Å R-free 0.263
3RV4 Crystal structure of E.coli biotin carboxylase R16E mutant in complex with Mg-ADP and bicarbonate Deposited 2011-05-05 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–449（449 aa）
Mutation：R16E ADP ADENOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 2 BCT BICARBONATE ION × 2 CS CESIUM ION × 2 CL CHLORIDE ION × 4 NA SODIUM ION × 4 GOL GLYCEROL × 2 MOH METHANOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；PEG3350, CsCl, methanol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 1.98 Å R-free 0.219
4HR7 Crystal Structure of Biotin Carboxyl Carrier Protein-Biotin Carboxylase Complex from E.coli Deposited 2012-10-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain A 1–449（449 aa）
Chain C 1–449（449 aa）
Chain E 1–449（449 aa）
Chain F 1–449（449 aa）
Not recorded SO4 SULFATE ION × 12 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；295.15 K；0.2 M ammonium sulfate, 0.1 M Bis-Tris, pH 6.5, 25% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 295.15K
Resolution 2.50 Å R-free 0.229
8UXZ E. coli acetyl-CoA carboxylase, wide stacked local reconstruction, 3.20 Angstrom Deposited 2023-11-11 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain C 1–446（446 aa）
Chain G 1–446（446 aa）
Not recorded BTN BIOTIN × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ZN ZINC ION × 2 ACO ACETYL COENZYME *A × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；2.5 mg/ml ACC complex in 50 mM HEPES pH 7.5, 100 mM bicarbonate, 7.5 mM ATP, 20 mM MgCl2 and 1 mM acetyl-CoA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8UZ2 E. coli acetyl-CoA carboxylase, narrow helical local reconstruction, 3.18 Angstrom Deposited 2023-11-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain C 1–446（446 aa）
Chain G 1–446（446 aa）
Not recorded BTN BIOTIN × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ZN ZINC ION × 2 ACO ACETYL COENZYME *A × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；2.5 mg/ml ACC complex in 50 mM HEPES pH 7.5, 100 mM bicarbonate, 7.5 mM ATP, 20 mM MgCl2 and 1 mM acetyl-CoA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.18 Å
9E4N E. coli acetyl-CoA carboxylase, narrow helical tube, 4.04 Angstrom Deposited 2024-10-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 152 PDB declaration: 152-meric
Chain C 1–449（449 aa）
Not recorded BTN BIOTIN × 38 ADP ADENOSINE-5'-DIPHOSPHATE × 38 MG MAGNESIUM ION × 38 ZN ZINC ION × 38 ACO ACETYL COENZYME *A × 38 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；2.5 mg/ml ACC complex in 50 mM HEPES pH 7.5, 100 mM bicarbonate, 7.5 mM ATP, 20 mM MgCl2 and 1 mM acetyl-CoA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.04 Å
9E4O E. coli acetyl-CoA carboxylase, wide stacked tube, 3.98 Angstrom Deposited 2024-10-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 160 PDB declaration: 160-meric
Chain C 1–449（449 aa）
Not recorded BTN BIOTIN × 40 ADP ADENOSINE-5'-DIPHOSPHATE × 40 MG MAGNESIUM ION × 40 ZN ZINC ION × 40 ACO ACETYL COENZYME *A × 40 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；2.5 mg/ml ACC complex in 50 mM HEPES pH 7.5, 100 mM bicarbonate, 7.5 mM ATP, 20 mM MgCl2 and 1 mM acetyl-CoA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.98 Å

29 other PDB entries and 49 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ACCC_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 22–470； UniProt 1–449 Author chain B； PDBConstruct 22–470； UniProt 1–449

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 3jzi

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3jzi
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3jzi
Deposition date deposition_date2009-09-23
Structure title titleCrystal structure of biotin carboxylase from E. Coli in complex with benzimidazole series
Keywords keywords;Biotin carboxylase; AccC; Acetyl coenzyme-A carboxylase; ACCase;, ATP-binding, Biotin, Fatty acid biosynthesis, Ligase, Lipid synthesis, Nucleotide-binding ;; LIGASE
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_guinier30.97 Å
Radius of gyration Rg (electron density) rg_electron30.37 Å
Forward intensity I(0) i0154184000.00
Molecular weight molecular_weight97996.0 kDa
Excluded volume excluded_volume122410 ų
Envelope volume envelope_volume147470 ų
Hydration-shell volume shell_volume40782 ų
Envelope diameter envelope_diameter120.9 Å
Shell Rg shell_rg37.11 Å
Envelope Rg envelope_rg30.63 Å
Shape Rg shape_rg30.36 Å
Total Rg total_rg30.96 Å
Total atoms total_atoms6880
Residues n_residues891
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 dmax113.9 Å
Rg (real space) rg_real31.11 Å
Rg uncertainty (real space) rg_real_error1.07 Å
I(0) (real space) i0_real1.5420e+08
I(0) uncertainty (real space) i0_real_error2.5430e+06
Rg (reciprocal space) rg_reciprocal31.05 Å
I(0) (reciprocal space) i0_reciprocal154200000.0000
Solution quality estimate total_estimate0.5895
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary35.7 Å
Skewness Skewness skewness0.557
Kurtosis Kurtosis kurtosis0.068
Angular range angular_range— – 0.2550 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha46430000.0000
Real-space data points n_real_points52
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.593; Stabil: 1.000; Sysdev: 0.040; Positv: 1.000; Valcen: 0.833; Smooth: 0.928
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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) 13 domains

SCOP 2.08 (7 domains)

Domain ID domain_idd3jzia1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.30 — PreATP-grasp domain
Superfamily Superfamily superfamilyc.30.1 — PreATP-grasp domain
Family Family familyc.30.1.1 — BC N-terminal domain-like
Domain ID domain_idd3jzia2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.142 — ATP-grasp
Superfamily Superfamily superfamilyd.142.1 — Glutathione synthetase ATP-binding domain-like
Family Family familyd.142.1.2 — BC ATP-binding domain-like
Domain ID domain_idd3jzia3
Class classb — All beta proteins
Fold Fold foldb.84 — Barrel-sandwich hybrid
Superfamily Superfamily superfamilyb.84.2 — Rudiment single hybrid motif
Family Family familyb.84.2.1 — BC C-terminal domain-like
Domain ID domain_idd3jzib1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.30 — PreATP-grasp domain
Superfamily Superfamily superfamilyc.30.1 — PreATP-grasp domain
Family Family familyc.30.1.1 — BC N-terminal domain-like
Domain ID domain_idd3jzib2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.142 — ATP-grasp
Superfamily Superfamily superfamilyd.142.1 — Glutathione synthetase ATP-binding domain-like
Family Family familyd.142.1.2 — BC ATP-binding domain-like
Domain ID domain_idd3jzib3
Class classb — All beta proteins
Fold Fold foldb.84 — Barrel-sandwich hybrid
Superfamily Superfamily superfamilyb.84.2 — Rudiment single hybrid motif
Family Family familyb.84.2.1 — BC C-terminal domain-like
Domain ID domain_idd3jzib4
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (6 domains)

Domain ID domain_id3jziA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily20 —
Domain ID domain_id3jziA02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology470 — D-amino Acid Aminotransferase; Chain A, domain 1
Homologous superfamily homologous superfamily20 — ATP-grasp fold, B domain
Domain ID domain_id3jziA03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily20 — ATP-grasp fold, A domain
Domain ID domain_id3jziB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily20 —
Domain ID domain_id3jziB02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology470 — D-amino Acid Aminotransferase; Chain A, domain 1
Homologous superfamily homologous superfamily20 — ATP-grasp fold, B domain
Domain ID domain_id3jziB03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily20 — ATP-grasp fold, A domain
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8. Citations (1)

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9. Files and Curves (10)