3dva

Snapshots of catalysis in the E1 subunit of the pyruvate dehydrogenase multi-enzyme complex

Method: X-RAY DIFFRACTION D_max: 164.2 Å Quality: GOOD

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

Pyruvate dehydrogenase E1 component subunit alpha

Bacillus stearothermophilus

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 heterocomplex Heteromer Protein × 5 PDB declaration: pentameric（5） Consistent with protein copy count	Chain A； UniProt 1–369 Chain C； UniProt 1–369	Mutation：I206A	Pyruvate dehydrogenase E1 component subunit beta × 2 （P21874） Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex × 1 （P11961） MG MAGNESIUM ION × 3 TPW 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-METHYLTHIOPHEN-2-YL}ETHYL TRIHYDROGEN DIPHOSPHATE × 2 K POTASSIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.5；291.15 K；The mutant crystals are obtained from sitting-drop vapour diffusion using following condition: 10-15% PEG 4K, 0.2 M imidazole malate pH 5 in the presence of 5 mM 3-deazaThDP, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K	Resolution 2.35 Å R-free 0.247
2	Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric（5） Consistent with protein copy count	Chain E； UniProt 1–369 Chain G； UniProt 1–369	Mutation：I206A	Pyruvate dehydrogenase E1 component subunit beta × 2 （P21874） Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex × 1 （P11961） MG MAGNESIUM ION × 3 TPW 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-METHYLTHIOPHEN-2-YL}ETHYL TRIHYDROGEN DIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.5；291.15 K；The mutant crystals are obtained from sitting-drop vapour diffusion using following condition: 10-15% PEG 4K, 0.2 M imidazole malate pH 5 in the presence of 5 mM 3-deazaThDP, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K	Resolution 2.35 Å R-free 0.247

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 3DVA	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1W85 The crystal structure of pyruvate dehydrogenase E1 bound to the peripheral subunit binding domain of E2 Deposited 2004-09-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 1–368（368 aa） Chain C 1–368（368 aa）	Not recorded	MG MAGNESIUM ION × 3 PEG DI(HYDROXYETHYL)ETHER × 2 TPP THIAMINE DIPHOSPHATE × 2 K POTASSIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；10% PEG 5500 MONOMETHYL ETHER, 0.2M IMIDAZOLE MALATE PH5. 20DEG C, SITTING-DROP., pH 5.00	Resolution 2.00 Å R-free 0.215
1W85 The crystal structure of pyruvate dehydrogenase E1 bound to the peripheral subunit binding domain of E2 Deposited 2004-09-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain E 1–368（368 aa） Chain G 1–368（368 aa）	Not recorded	MG MAGNESIUM ION × 3 PEG DI(HYDROXYETHYL)ETHER × 1 TPP THIAMINE DIPHOSPHATE × 2 K POTASSIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；10% PEG 5500 MONOMETHYL ETHER, 0.2M IMIDAZOLE MALATE PH5. 20DEG C, SITTING-DROP., pH 5.00	Resolution 2.00 Å R-free 0.215
1W88 The crystal structure of pyruvate dehydrogenase E1(D180N,E183Q) bound to the peripheral subunit binding domain of E2 Deposited 2004-09-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 1–368（368 aa） Chain C 1–368（368 aa）	Mutation：YES Mutation：YES	MG MAGNESIUM ION × 2 TPP THIAMINE DIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 5；15% PEG 4000, 0.2M IMIDAZOLE MALATE PH5, pH 5.00	Resolution 2.30 Å R-free 0.262
1W88 The crystal structure of pyruvate dehydrogenase E1(D180N,E183Q) bound to the peripheral subunit binding domain of E2 Deposited 2004-09-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain E 1–368（368 aa） Chain G 1–368（368 aa）	Mutation：YES Mutation：YES	MG MAGNESIUM ION × 2 TPP THIAMINE DIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 5；15% PEG 4000, 0.2M IMIDAZOLE MALATE PH5, pH 5.00	Resolution 2.30 Å R-free 0.262
3DUF Snapshots of catalysis in the E1 subunit of the pyruvate dehydrogenase multi-enzyme complex Deposited 2008-07-17	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 1–369（369 aa） Chain C 1–369（369 aa）	Not recorded	MG MAGNESIUM ION × 3 R1T 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-5-[(1R)-1-HYDROXYETHYL]-3-METHYL-2-THIENYL}ETHYL TRIHYDROGEN DIPHOSPHATE × 2 K POTASSIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291.15 K；The protein solution was then mixed in 1:1 volume ratio of crystallization buffer consisting of 8-12 % mono-methyl ether polyethylene glycol (MME PEG) 5000, 0.1 M Na maleate pH 5.5, and the droplet was left to equilibrate against a reservoir of neat crystallization buffer., VAPOR DIFFUSION, SITTING DROP, temperature 291.15K	Resolution 2.50 Å R-free 0.263
3DUF Snapshots of catalysis in the E1 subunit of the pyruvate dehydrogenase multi-enzyme complex Deposited 2008-07-17	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain E 1–369（369 aa） Chain G 1–369（369 aa）	Not recorded	MG MAGNESIUM ION × 2 R1T 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-5-[(1R)-1-HYDROXYETHYL]-3-METHYL-2-THIENYL}ETHYL TRIHYDROGEN DIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291.15 K；The protein solution was then mixed in 1:1 volume ratio of crystallization buffer consisting of 8-12 % mono-methyl ether polyethylene glycol (MME PEG) 5000, 0.1 M Na maleate pH 5.5, and the droplet was left to equilibrate against a reservoir of neat crystallization buffer., VAPOR DIFFUSION, SITTING DROP, temperature 291.15K	Resolution 2.50 Å R-free 0.263
3DV0 Snapshots of catalysis in the E1 subunit of the pyruvate dehydrogenase multi-enzyme complex Deposited 2008-07-18	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 1–369（369 aa） Chain C 1–369（369 aa）	Not recorded	MG MAGNESIUM ION × 3 TPW 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-METHYLTHIOPHEN-2-YL}ETHYL TRIHYDROGEN DIPHOSPHATE × 2 K POTASSIUM ION × 2 PYR PYRUVIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291.15 K；10-15% PEG 4K, 0.2 M imidazole malate pH 5 in the presence of 5 mM 3-deazaThDP. The crystals were soaked with 10mM pyruvate for 3-day, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K	Resolution 2.50 Å R-free 0.241
3DV0 Snapshots of catalysis in the E1 subunit of the pyruvate dehydrogenase multi-enzyme complex Deposited 2008-07-18	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain E 1–369（369 aa） Chain G 1–369（369 aa）	Not recorded	MG MAGNESIUM ION × 3 TPW 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-METHYLTHIOPHEN-2-YL}ETHYL TRIHYDROGEN DIPHOSPHATE × 2 K POTASSIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291.15 K；10-15% PEG 4K, 0.2 M imidazole malate pH 5 in the presence of 5 mM 3-deazaThDP. The crystals were soaked with 10mM pyruvate for 3-day, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K	Resolution 2.50 Å R-free 0.241

4 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ODPA_BACST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–369； UniProt 1–369 Author chain C； PDBConstruct 1–369； UniProt 1–369 Author chain E； PDBConstruct 1–369； UniProt 1–369 Author chain G； PDBConstruct 1–369； UniProt 1–369

Pyruvate dehydrogenase E1 component subunit beta

Bacillus stearothermophilus

UniProt P21874

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 heterocomplex Heteromer Protein × 5 PDB declaration: pentameric（5） Consistent with protein copy count	Chain B； UniProt 1–325 Chain D； UniProt 1–325	Not recorded	Pyruvate dehydrogenase E1 component subunit alpha × 2 （P21873） Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex × 1 （P11961） MG MAGNESIUM ION × 3 TPW 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-METHYLTHIOPHEN-2-YL}ETHYL TRIHYDROGEN DIPHOSPHATE × 2 K POTASSIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.5；291.15 K；The mutant crystals are obtained from sitting-drop vapour diffusion using following condition: 10-15% PEG 4K, 0.2 M imidazole malate pH 5 in the presence of 5 mM 3-deazaThDP, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K	Resolution 2.35 Å R-free 0.247
2	Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric（5） Consistent with protein copy count	Chain F； UniProt 1–325 Chain H； UniProt 1–325	Not recorded	Pyruvate dehydrogenase E1 component subunit alpha × 2 （P21873） Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex × 1 （P11961） MG MAGNESIUM ION × 3 TPW 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-METHYLTHIOPHEN-2-YL}ETHYL TRIHYDROGEN DIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.5；291.15 K；The mutant crystals are obtained from sitting-drop vapour diffusion using following condition: 10-15% PEG 4K, 0.2 M imidazole malate pH 5 in the presence of 5 mM 3-deazaThDP, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K	Resolution 2.35 Å R-free 0.247

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 3DVA	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1W85 The crystal structure of pyruvate dehydrogenase E1 bound to the peripheral subunit binding domain of E2 Deposited 2004-09-16	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain B 1–324（324 aa） Chain D 1–324（324 aa）	Not recorded	MG MAGNESIUM ION × 3 PEG DI(HYDROXYETHYL)ETHER × 2 TPP THIAMINE DIPHOSPHATE × 2 K POTASSIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；10% PEG 5500 MONOMETHYL ETHER, 0.2M IMIDAZOLE MALATE PH5. 20DEG C, SITTING-DROP., pH 5.00	Resolution 2.00 Å R-free 0.215
1W85 The crystal structure of pyruvate dehydrogenase E1 bound to the peripheral subunit binding domain of E2 Deposited 2004-09-16	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain F 1–324（324 aa） Chain H 1–324（324 aa）	Not recorded	MG MAGNESIUM ION × 3 PEG DI(HYDROXYETHYL)ETHER × 1 TPP THIAMINE DIPHOSPHATE × 2 K POTASSIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；10% PEG 5500 MONOMETHYL ETHER, 0.2M IMIDAZOLE MALATE PH5. 20DEG C, SITTING-DROP., pH 5.00	Resolution 2.00 Å R-free 0.215
1W88 The crystal structure of pyruvate dehydrogenase E1(D180N,E183Q) bound to the peripheral subunit binding domain of E2 Deposited 2004-09-16	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain B 1–324（324 aa） Chain D 1–324（324 aa）	Not recorded	MG MAGNESIUM ION × 2 TPP THIAMINE DIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 5；15% PEG 4000, 0.2M IMIDAZOLE MALATE PH5, pH 5.00	Resolution 2.30 Å R-free 0.262
1W88 The crystal structure of pyruvate dehydrogenase E1(D180N,E183Q) bound to the peripheral subunit binding domain of E2 Deposited 2004-09-16	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain F 1–324（324 aa） Chain H 1–324（324 aa）	Not recorded	MG MAGNESIUM ION × 2 TPP THIAMINE DIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 5；15% PEG 4000, 0.2M IMIDAZOLE MALATE PH5, pH 5.00	Resolution 2.30 Å R-free 0.262
3DUF Snapshots of catalysis in the E1 subunit of the pyruvate dehydrogenase multi-enzyme complex Deposited 2008-07-17	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain B 1–325（325 aa） Chain D 1–325（325 aa）	Not recorded	MG MAGNESIUM ION × 3 R1T 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-5-[(1R)-1-HYDROXYETHYL]-3-METHYL-2-THIENYL}ETHYL TRIHYDROGEN DIPHOSPHATE × 2 K POTASSIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291.15 K；The protein solution was then mixed in 1:1 volume ratio of crystallization buffer consisting of 8-12 % mono-methyl ether polyethylene glycol (MME PEG) 5000, 0.1 M Na maleate pH 5.5, and the droplet was left to equilibrate against a reservoir of neat crystallization buffer., VAPOR DIFFUSION, SITTING DROP, temperature 291.15K	Resolution 2.50 Å R-free 0.263
3DUF Snapshots of catalysis in the E1 subunit of the pyruvate dehydrogenase multi-enzyme complex Deposited 2008-07-17	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain F 1–325（325 aa） Chain H 1–325（325 aa）	Not recorded	MG MAGNESIUM ION × 2 R1T 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-5-[(1R)-1-HYDROXYETHYL]-3-METHYL-2-THIENYL}ETHYL TRIHYDROGEN DIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291.15 K；The protein solution was then mixed in 1:1 volume ratio of crystallization buffer consisting of 8-12 % mono-methyl ether polyethylene glycol (MME PEG) 5000, 0.1 M Na maleate pH 5.5, and the droplet was left to equilibrate against a reservoir of neat crystallization buffer., VAPOR DIFFUSION, SITTING DROP, temperature 291.15K	Resolution 2.50 Å R-free 0.263
3DV0 Snapshots of catalysis in the E1 subunit of the pyruvate dehydrogenase multi-enzyme complex Deposited 2008-07-18	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain B 1–325（325 aa） Chain D 1–325（325 aa）	Not recorded	MG MAGNESIUM ION × 3 TPW 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-METHYLTHIOPHEN-2-YL}ETHYL TRIHYDROGEN DIPHOSPHATE × 2 K POTASSIUM ION × 2 PYR PYRUVIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291.15 K；10-15% PEG 4K, 0.2 M imidazole malate pH 5 in the presence of 5 mM 3-deazaThDP. The crystals were soaked with 10mM pyruvate for 3-day, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K	Resolution 2.50 Å R-free 0.241
3DV0 Snapshots of catalysis in the E1 subunit of the pyruvate dehydrogenase multi-enzyme complex Deposited 2008-07-18	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain F 1–325（325 aa） Chain H 1–325（325 aa）	Not recorded	MG MAGNESIUM ION × 3 TPW 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-METHYLTHIOPHEN-2-YL}ETHYL TRIHYDROGEN DIPHOSPHATE × 2 K POTASSIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291.15 K；10-15% PEG 4K, 0.2 M imidazole malate pH 5 in the presence of 5 mM 3-deazaThDP. The crystals were soaked with 10mM pyruvate for 3-day, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K	Resolution 2.50 Å R-free 0.241

4 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ODPB_BACST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–325； UniProt 1–325 Author chain D； PDBConstruct 1–325； UniProt 1–325 Author chain F； PDBConstruct 1–325； UniProt 1–325 Author chain H； PDBConstruct 1–325； UniProt 1–325

Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex

Bacillus stearothermophilus

UniProt P11961

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 heterocomplex Heteromer Protein × 5 PDB declaration: pentameric（5） Consistent with protein copy count	Chain I； UniProt 1–428	Not recorded	Pyruvate dehydrogenase E1 component subunit alpha × 2 （P21873） Pyruvate dehydrogenase E1 component subunit beta × 2 （P21874） MG MAGNESIUM ION × 3 TPW 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-METHYLTHIOPHEN-2-YL}ETHYL TRIHYDROGEN DIPHOSPHATE × 2 K POTASSIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.5；291.15 K；The mutant crystals are obtained from sitting-drop vapour diffusion using following condition: 10-15% PEG 4K, 0.2 M imidazole malate pH 5 in the presence of 5 mM 3-deazaThDP, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K	Resolution 2.35 Å R-free 0.247
2	Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric（5） Consistent with protein copy count	Chain J； UniProt 1–428	Not recorded	Pyruvate dehydrogenase E1 component subunit alpha × 2 （P21873） Pyruvate dehydrogenase E1 component subunit beta × 2 （P21874） MG MAGNESIUM ION × 3 TPW 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-METHYLTHIOPHEN-2-YL}ETHYL TRIHYDROGEN DIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.5；291.15 K；The mutant crystals are obtained from sitting-drop vapour diffusion using following condition: 10-15% PEG 4K, 0.2 M imidazole malate pH 5 in the presence of 5 mM 3-deazaThDP, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K	Resolution 2.35 Å R-free 0.247

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 3DVA	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1B5S DIHYDROLIPOYL TRANSACETYLASE (E.C.2.3.1.12) CATALYTIC DOMAIN (RESIDUES 184-425) FROM BACILLUS STEAROTHERMOPHILUS Deposited 1999-01-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 60 PDB declaration: 60-meric	Chain A 184–425（242 aa） Fragment：CATALYTIC DOMAIN Chain B 184–425（242 aa） Fragment：CATALYTIC DOMAIN Chain C 184–425（242 aa） Fragment：CATALYTIC DOMAIN Chain D 184–425（242 aa） Fragment：CATALYTIC DOMAIN Chain E 184–425（242 aa） Fragment：CATALYTIC DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7	Resolution 4.40 Å
1EBD DIHYDROLIPOAMIDE DEHYDROGENASE COMPLEXED WITH THE BINDING DOMAIN OF THE DIHYDROLIPOAMIDE ACETYLASE Deposited 1996-02-03	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 129–169（41 aa） Fragment：BINDING DOMAIN, RESIDUES 130 - 170	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.60 Å
1LAB THREE-DIMENSIONAL STRUCTURE OF THE LIPOYL DOMAIN FROM BACILLUS STEAROTHERMOPHILUS PYRUVATE DEHYDROGENASE MULTIENZYME COMPLEX Deposited 1992-09-02	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–80（80 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1LAC THREE-DIMENSIONAL STRUCTURE OF THE LIPOYL DOMAIN FROM BACILLUS STEAROTHERMOPHILUS PYRUVATE DEHYDROGENASE MULTIENZYME COMPLEX Deposited 1992-09-02	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–80（80 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1W3D NMR structure of the peripheral-subunit binding domain of Bacillus stearothermophilus E2p Deposited 2004-07-14	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 118–170（53 aa） Fragment：RESIDUES 118-170	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 20	Resolution not provided
1W4E Peripheral-subunit binding domains from mesophilic, thermophilic, and hyperthermophilic bacteria fold by ultrafast, apparently two-state transitions Deposited 2004-07-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 125–169（45 aa） Fragment：RESIDUES 125-169	Mutation：YES	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.5；298 K；Ionic strength (raw mmCIF value) 150；Pressure 1.0 NMR sample composition 95% WATER/5% D2O, 3MM SAMPLE	Resolution not provided
1W4F Peripheral-subunit from mesophilic, thermophilic and hyperthermophilic bacteria fold by ultrafast, apparently two-state transitions Deposited 2004-07-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 125–169（45 aa） Fragment：RESIDUES 125-169	Mutation：YES	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.5；298 K；Ionic strength (raw mmCIF value) 150；Pressure 1.0 NMR sample composition 95% H20/5%D20, 3MM SAMPLE	Resolution not provided
1W4G Peripheral-subunit binding domains from mesophilic, thermophilic, and hyperthermophilic bacteria fold by ultrafast, apparently two-state folding transitions Deposited 2004-07-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 125–169（45 aa） Fragment：RESIDUES 125-169	Mutation：YES	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.5；298 K；Ionic strength (raw mmCIF value) 150；Pressure 1.0 NMR sample composition 95% WATER/5% D2O, 3MM SAMPLE	Resolution not provided
1W4H Peripheral-subunit from mesophilic, thermophilic and hyperthermophilic bacteria fold by ultrafast, apparently two-state transitions Deposited 2004-07-23	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 108–152（45 aa） Fragment：RESIDUES 108-152	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 200；Pressure 1.0 NMR sample composition 95%WATER/5% D20, 3MM SAMPLE	Resolution not provided
1W85 The crystal structure of pyruvate dehydrogenase E1 bound to the peripheral subunit binding domain of E2 Deposited 2004-09-16	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain I 122–170（49 aa） Fragment：PERIPHERAL SUBUNIT BINDING DOMAIN (PSBD), RESIDUES 122-170	Not recorded	MG MAGNESIUM ION × 3 PEG DI(HYDROXYETHYL)ETHER × 2 TPP THIAMINE DIPHOSPHATE × 2 K POTASSIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；10% PEG 5500 MONOMETHYL ETHER, 0.2M IMIDAZOLE MALATE PH5. 20DEG C, SITTING-DROP., pH 5.00	Resolution 2.00 Å R-free 0.215
1W85 The crystal structure of pyruvate dehydrogenase E1 bound to the peripheral subunit binding domain of E2 Deposited 2004-09-16	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain J 122–170（49 aa） Fragment：PERIPHERAL SUBUNIT BINDING DOMAIN (PSBD), RESIDUES 122-170	Not recorded	MG MAGNESIUM ION × 3 PEG DI(HYDROXYETHYL)ETHER × 1 TPP THIAMINE DIPHOSPHATE × 2 K POTASSIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；10% PEG 5500 MONOMETHYL ETHER, 0.2M IMIDAZOLE MALATE PH5. 20DEG C, SITTING-DROP., pH 5.00	Resolution 2.00 Å R-free 0.215
1W88 The crystal structure of pyruvate dehydrogenase E1(D180N,E183Q) bound to the peripheral subunit binding domain of E2 Deposited 2004-09-16	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain I 122–170（49 aa） Fragment：PERIPHERAL SUBUNIT BINDING DOMAIN (PSBD), RESIDUES 127-169	Not recorded	MG MAGNESIUM ION × 2 TPP THIAMINE DIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 5；15% PEG 4000, 0.2M IMIDAZOLE MALATE PH5, pH 5.00	Resolution 2.30 Å R-free 0.262
1W88 The crystal structure of pyruvate dehydrogenase E1(D180N,E183Q) bound to the peripheral subunit binding domain of E2 Deposited 2004-09-16	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain J 122–170（49 aa） Fragment：PERIPHERAL SUBUNIT BINDING DOMAIN (PSBD), RESIDUES 127-169	Not recorded	MG MAGNESIUM ION × 2 TPP THIAMINE DIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 5；15% PEG 4000, 0.2M IMIDAZOLE MALATE PH5, pH 5.00	Resolution 2.30 Å R-free 0.262
2PDD THE HIGH RESOLUTION STRUCTURE OF THE PERIPHERAL SUBUNIT-BINDING DOMAIN OF DIHYDROLIPOAMIDE ACETYLTRANSFERASE FROM THE PYRUVATE DEHYDROGENASE MULTIENZYME COMPLEX OF BACILLUS STEAROTHERMOPHILUS Deposited 1992-11-25	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 128–170（43 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
2PDE THE HIGH RESOLUTION STRUCTURE OF THE PERIPHERAL SUBUNIT-BINDING DOMAIN OF DIHYDROLIPOAMIDE ACETYLTRANSFERASE FROM THE PYRUVATE DEHYDROGENASE MULTIENZYME COMPLEX OF BACILLUS STEAROTHERMOPHILUS Deposited 1992-11-25	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 128–170（43 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
3DUF Snapshots of catalysis in the E1 subunit of the pyruvate dehydrogenase multi-enzyme complex Deposited 2008-07-17	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain I 1–428（428 aa）	Not recorded	MG MAGNESIUM ION × 3 R1T 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-5-[(1R)-1-HYDROXYETHYL]-3-METHYL-2-THIENYL}ETHYL TRIHYDROGEN DIPHOSPHATE × 2 K POTASSIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291.15 K；The protein solution was then mixed in 1:1 volume ratio of crystallization buffer consisting of 8-12 % mono-methyl ether polyethylene glycol (MME PEG) 5000, 0.1 M Na maleate pH 5.5, and the droplet was left to equilibrate against a reservoir of neat crystallization buffer., VAPOR DIFFUSION, SITTING DROP, temperature 291.15K	Resolution 2.50 Å R-free 0.263
3DUF Snapshots of catalysis in the E1 subunit of the pyruvate dehydrogenase multi-enzyme complex Deposited 2008-07-17	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain J 1–428（428 aa）	Not recorded	MG MAGNESIUM ION × 2 R1T 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-5-[(1R)-1-HYDROXYETHYL]-3-METHYL-2-THIENYL}ETHYL TRIHYDROGEN DIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291.15 K；The protein solution was then mixed in 1:1 volume ratio of crystallization buffer consisting of 8-12 % mono-methyl ether polyethylene glycol (MME PEG) 5000, 0.1 M Na maleate pH 5.5, and the droplet was left to equilibrate against a reservoir of neat crystallization buffer., VAPOR DIFFUSION, SITTING DROP, temperature 291.15K	Resolution 2.50 Å R-free 0.263
3DV0 Snapshots of catalysis in the E1 subunit of the pyruvate dehydrogenase multi-enzyme complex Deposited 2008-07-18	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain I 1–428（428 aa）	Not recorded	MG MAGNESIUM ION × 3 TPW 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-METHYLTHIOPHEN-2-YL}ETHYL TRIHYDROGEN DIPHOSPHATE × 2 K POTASSIUM ION × 2 PYR PYRUVIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291.15 K；10-15% PEG 4K, 0.2 M imidazole malate pH 5 in the presence of 5 mM 3-deazaThDP. The crystals were soaked with 10mM pyruvate for 3-day, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K	Resolution 2.50 Å R-free 0.241
3DV0 Snapshots of catalysis in the E1 subunit of the pyruvate dehydrogenase multi-enzyme complex Deposited 2008-07-18	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain J 1–428（428 aa）	Not recorded	MG MAGNESIUM ION × 3 TPW 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-METHYLTHIOPHEN-2-YL}ETHYL TRIHYDROGEN DIPHOSPHATE × 2 K POTASSIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291.15 K；10-15% PEG 4K, 0.2 M imidazole malate pH 5 in the presence of 5 mM 3-deazaThDP. The crystals were soaked with 10mM pyruvate for 3-day, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K	Resolution 2.50 Å R-free 0.241
9UKZ dihydrolipoyl acetyl transferase (E2) inner core of the pyruvate dehydrogenase complex Deposited 2025-04-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 185–426（242 aa） Chain B 185–426（242 aa） Chain C 185–426（242 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.20 Å

16 other PDB entries and 20 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ODP2_BACST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain I； PDBConstruct 1–428； UniProt 1–428 Author chain J； PDBConstruct 1–428； UniProt 1–428

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	3dva
Deposition date deposition_date	2008-07-18
Structure title title	Snapshots of catalysis in the E1 subunit of the pyruvate dehydrogenase multi-enzyme complex
Keywords keywords	;Oxidoreductase, PYRUVATE, DEHYDROGENASE, DIHYDROLIPOYL, ACETYL TRANSFERASE, MULTIENZYME COMPLEX, TRANSFERASE, Glycolysis, Phosphoprotein, Thiamine pyrophosphate, Acyltransferase, OXIDOREDUCTASE-TRANSFERASE COMPLEX ;; OXIDOREDUCTASE/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	48.51 Å
Radius of gyration Rg (electron density) rg_electron	48.45 Å
Forward intensity I(0) i0	1367570000.00
Molecular weight molecular_weight	314340.0 kDa
Excluded volume excluded_volume	395740 Å³
Envelope volume envelope_volume	491750 Å³
Hydration-shell volume shell_volume	83084 Å³
Envelope diameter envelope_diameter	179.3 Å
Shell Rg shell_rg	53.30 Å
Envelope Rg envelope_rg	48.38 Å
Shape Rg shape_rg	48.43 Å
Total Rg total_rg	48.66 Å
Total atoms total_atoms	22155
Residues n_residues	2827
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	164.2 Å
Rg (real space) rg_real	48.69 Å
Rg uncertainty (real space) rg_real_error	1.47 Å
I(0) (real space) i0_real	1.3680e+09
I(0) uncertainty (real space) i0_real_error	2.9250e+07
Rg (reciprocal space) rg_reciprocal	48.51 Å
I(0) (reciprocal space) i0_reciprocal	1367000000.0000
Solution quality estimate total_estimate	0.8609
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	51.3 Å
Skewness Skewness skewness	0.415
Kurtosis Kurtosis kurtosis	-0.384
Angular range angular_range	— – 0.1600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	266300000.0000
Real-space data points n_real_points	33
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.841; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.981; Smooth: 0.682

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Pyruvate dehydrogenase E1 component subunit alpha
Molecular weight formula_weight	41476.1 kDa
EC 编号 ec_number	1.2.4.1
Mutation mutation	I206A
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G
Atom count atom_count	23282

MGVKTFQFPFAEQLEKVAEQFPTFQILNEEGEVVNEEAMPELSDEQLKELMRRMVYTRILDQRSISLNRQGRLGFYAPTAGQEASQIASHFALEKEDFILPGYRDVPQIIWHGLPLYQAFLFSRGHFHGNQIPEGVNVLPPQIIIGAQYIQAAGVALGLKMRGKKAVAITYTGDGGTSQGDFYEGINFAGAFKAPAIFVVQNNRFAASTPVEKQTVAKTLAQKAVAAGIPGIQVDGMDPLAVYAAVKAARERAINGEGPTLIETLCFRYGPHTMSGDDPTRYRSKELENEWAKKDPLVRFRKFLEAKGLWSEEEENNVIEQAKEEIKEAIKKADETPKQKVTDLISIMFEELPFNLKEQYEIYKEKESK

来源 Source

来源生物 organism	Bacillus stearothermophilus
NCBI Class编号 ncbi_taxonomy_id	1422
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Pyruvate dehydrogenase E1 component subunit beta
Molecular weight formula_weight	35495.6 kDa
EC 编号 ec_number	1.2.4.1
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,F,H

MAQMTMVQAITDALRIELKNDPNVLIFGEDVGVNGGVFRATEGLQAEFGEDRVFDTPLAESGIGGLAIGLALQGFRPVPEIQFFGFVYEVMDSICGQMARIRYRTGGRYHMPITIRSPFGGGVHTPELHSDSLEGLVAQQPGLKVVIPSTPYDAKGLLISAIRDNDPVIFLEHLKLYRSFRQEVPEGEYTIPIGKADIKREGKDITIIAYGAMVHESLKAAAELEKEGISAEVVDLRTVQPLDIETIIGSVEKTGRAIVVQEAQRQAGIAANVVAEINERAILSLEAPVLRVAAPDTVYPFAQAESVWLPNFKDVIETAKKVMNF

来源 Source

来源生物 organism	Bacillus stearothermophilus
NCBI Class编号 ncbi_taxonomy_id	1422
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex
Molecular weight formula_weight	46392.2 kDa
EC 编号 ec_number	2.3.1.12
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I,J

MAFEFKLPDIGEGIHEGEIVKWFVKPGDEVNEDDVLCEVQNDKAVVEIPSPVKGKVLEILVPEGTVATVGQTLITLDAPGYENMTFKGQEQEEAKKEEKTETVSKEEKVDAVAPNAPAAEAEAGPNRRVIAMPSVRKYAREKGVDIRLVQGTGKNGRVLKEDIDAFLAGGAKPAPAAAEEKAAPAAAKPATTEGEFPETREKMSGIRRAIAKAMVHSKHTAPHVTLMDEADVTKLVAHRKKFKAIAAEKGIKLTFLPYVVKALVSALREYPVLNTSIDDETEEIIQKHYYNIGIAADTDRGLLVPVIKHADRKPIFALAQEINELAEKARDGKLTPGEMKGASCTITNIGSAGGQWFTPVINHPEVAILGIGRIAEKPIVRDGEIVAAPMLALSLSFDHRMIDGATAQKALNHIKRLLSDPELLLMEA

来源 Source

来源生物 organism	Bacillus stearothermophilus
NCBI Class编号 ncbi_taxonomy_id	1422
宿主生物 host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 5 Entity 5 non-polymer

Description description	2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-METHYLTHIOPHEN-2-YL}ETHYL TRIHYDROGEN DIPHOSPHATE
Molecular weight formula_weight	423.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1127

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7. Fold Classification (SCOP + CATH) 28 domains

SCOP 2.08 (14 domains)

Domain ID domain_id	d3dvaa_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.36 — Thiamin diphosphate-binding fold (THDP-binding)
Superfamily Superfamily superfamily	c.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
Family Family family	c.36.1.11 — Branched-chain alpha-keto acid dehydrogenase PP module

Domain ID domain_id	d3dvab1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.36 — Thiamin diphosphate-binding fold (THDP-binding)
Superfamily Superfamily superfamily	c.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
Family Family family	c.36.1.0 — automated matches

Domain ID domain_id	d3dvab2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.48 — TK C-terminal domain-like
Superfamily Superfamily superfamily	c.48.1 — TK C-terminal domain-like
Family Family family	c.48.1.0 — automated matches

Domain ID domain_id	d3dvac_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.36 — Thiamin diphosphate-binding fold (THDP-binding)
Superfamily Superfamily superfamily	c.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
Family Family family	c.36.1.11 — Branched-chain alpha-keto acid dehydrogenase PP module

Domain ID domain_id	d3dvad1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.36 — Thiamin diphosphate-binding fold (THDP-binding)
Superfamily Superfamily superfamily	c.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
Family Family family	c.36.1.0 — automated matches

Domain ID domain_id	d3dvad2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.48 — TK C-terminal domain-like
Superfamily Superfamily superfamily	c.48.1 — TK C-terminal domain-like
Family Family family	c.48.1.0 — automated matches

Domain ID domain_id	d3dvae_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.36 — Thiamin diphosphate-binding fold (THDP-binding)
Superfamily Superfamily superfamily	c.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
Family Family family	c.36.1.11 — Branched-chain alpha-keto acid dehydrogenase PP module

Domain ID domain_id	d3dvaf1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.36 — Thiamin diphosphate-binding fold (THDP-binding)
Superfamily Superfamily superfamily	c.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
Family Family family	c.36.1.0 — automated matches

Domain ID domain_id	d3dvaf2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.48 — TK C-terminal domain-like
Superfamily Superfamily superfamily	c.48.1 — TK C-terminal domain-like
Family Family family	c.48.1.0 — automated matches

Domain ID domain_id	d3dvag_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.36 — Thiamin diphosphate-binding fold (THDP-binding)
Superfamily Superfamily superfamily	c.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
Family Family family	c.36.1.11 — Branched-chain alpha-keto acid dehydrogenase PP module

Domain ID domain_id	d3dvah1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.36 — Thiamin diphosphate-binding fold (THDP-binding)
Superfamily Superfamily superfamily	c.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
Family Family family	c.36.1.0 — automated matches

Domain ID domain_id	d3dvah2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.48 — TK C-terminal domain-like
Superfamily Superfamily superfamily	c.48.1 — TK C-terminal domain-like
Family Family family	c.48.1.0 — automated matches

Domain ID domain_id	d3dvai_
Class class	a — All alpha proteins
Fold Fold fold	a.9 — Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex
Superfamily Superfamily superfamily	a.9.1 — Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex
Family Family family	a.9.1.0 — automated matches

Domain ID domain_id	d3dvaj_
Class class	a — All alpha proteins
Fold Fold fold	a.9 — Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex
Superfamily Superfamily superfamily	a.9.1 — Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex
Family Family family	a.9.1.0 — automated matches

CATH v4.4 (14 domains)

Domain ID domain_id	3dvaA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains

Domain ID domain_id	3dvaB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains

Domain ID domain_id	3dvaB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	920 —

Domain ID domain_id	3dvaC00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains

Domain ID domain_id	3dvaD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains

Domain ID domain_id	3dvaD02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	920 —

Domain ID domain_id	3dvaE00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains

Domain ID domain_id	3dvaF01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains

Domain ID domain_id	3dvaF02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	920 —

Domain ID domain_id	3dvaG00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains

Domain ID domain_id	3dvaH01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains

Domain ID domain_id	3dvaH02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	920 —

Domain ID domain_id	3dvaI00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	320 — Dihydrolipoamide Transferase
Homologous superfamily homologous superfamily	10 — E3-binding domain

Domain ID domain_id	3dvaJ00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	320 — Dihydrolipoamide Transferase
Homologous superfamily homologous superfamily	10 — E3-binding domain

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8. Citations (1)

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Unit-cell length a length_a	68.673 Å
Unit-cell length b length_b	232.294 Å
Unit-cell length c length_c	91.936 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.20 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.350 Å
Low-resolution limit resolution_low	72.170 Å
R factor r_factor	0.1925
R_work r_work	0.1896
R_free r_free	0.2472

fit	/app/data/saxs_computation/dv/3dva/3dva.fit
pddf	/app/data/pr_computation/dv/3dva/3dva.pr.out
profile	/app/data/saxs_computation/dv/3dva/3dva.dat

Snapshots of catalysis in the E1 subunit of the pyruvate dehydrogenase multi-enzyme complex

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

Pyruvate dehydrogenase E1 component subunit alpha

State in the Current Structure

Other States of the Same Protein in the Database

Pyruvate dehydrogenase E1 component subunit beta

State in the Current Structure

Other States of the Same Protein in the Database

Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Fold Classification (SCOP + CATH) 28 domains

SCOP 2.08 (14 domains)

CATH v4.4 (14 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)