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2pdd

THE HIGH RESOLUTION STRUCTURE OF THE PERIPHERAL SUBUNIT-BINDING DOMAIN OF DIHYDROLIPOAMIDE ACETYLTRANSFERASE FROM THE PYRUVATE DEHYDROGENASE MULTIENZYME COMPLEX OF BACILLUS STEAROTHERMOPHILUS

Method: SOLUTION NMR Dmax: 34.1 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

DIHYDROLIPOAMIDE ACETYLTRANSFERASE

OrganismNot specified

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 128–170 Not recorded No other associated polymer SOLUTION NMR mmCIF provides none of the parsed experimental conditions Resolution not provided

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 2PDD 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 experimental method 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 method 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 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 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 experimental conditions 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 experimental conditions 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 experimental conditions 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 experimental conditions 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 experimental conditions 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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
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 Parsed fields agree 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 construct Different oligomeric state Different ligand/ion Different experimental method 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 construct Different oligomeric state Different ligand/ion Different experimental method 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 construct Different oligomeric state Different ligand/ion Different experimental method 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 construct Different oligomeric state Different ligand/ion Different experimental method 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
3DVA Snapshots of catalysis in the E1 subunit of the pyruvate dehydrogenase multi-enzyme complex Deposited 2008-07-18 Different construct Different oligomeric state Different ligand/ion Different experimental method 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 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
3DVA Snapshots of catalysis in the E1 subunit of the pyruvate dehydrogenase multi-enzyme complex Deposited 2008-07-18 Different construct Different oligomeric state Different ligand/ion Different experimental method 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 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
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 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 21 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ODP2_BACST
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–43； UniProt 128–170

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 2pdd

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2pdd
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2pdd
Deposition date deposition_date1992-11-25
Structure title titleTHE HIGH RESOLUTION STRUCTURE OF THE PERIPHERAL SUBUNIT-BINDING DOMAIN OF DIHYDROLIPOAMIDE ACETYLTRANSFERASE FROM THE PYRUVATE DEHYDROGENASE MULTIENZYME COMPLEX OF BACILLUS STEAROTHERMOPHILUS
Keywords keywordsOXIDO-REDUCTASE(ACYLTRANSFERASE), OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier9.54 Å
Radius of gyration Rg (electron density) rg_electron9.58 Å
Forward intensity I(0) i0339733000.00
Molecular weight molecular_weight158280.0 kDa
Excluded volume excluded_volume199990 ų
Envelope volume envelope_volume13224 ų
Hydration-shell volume shell_volume9540 ų
Envelope diameter envelope_diameter40.6 Å
Shell Rg shell_rg17.56 Å
Envelope Rg envelope_rg12.44 Å
Shape Rg shape_rg9.52 Å
Total Rg total_rg9.94 Å
Total atoms total_atoms22969
Residues n_residues1488
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 dmax34.1 Å
Rg (real space) rg_real9.48 Å
Rg uncertainty (real space) rg_real_error0.30 Å
I(0) (real space) i0_real3.3970e+08
I(0) uncertainty (real space) i0_real_error3.5650e+06
Rg (reciprocal space) rg_reciprocal9.48 Å
I(0) (reciprocal space) i0_reciprocal339700000.0000
Solution quality estimate total_estimate0.7924
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary12.9 Å
Skewness Skewness skewness0.024
Kurtosis Kurtosis kurtosis-0.086
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha36360.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.469; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.891
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd2pdda_
Class classa — All alpha proteins
Fold Fold folda.9 — Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex
Superfamily Superfamily superfamilya.9.1 — Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex
Family Family familya.9.1.1 — Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex

CATH v4.4 (1 domains)

Domain ID domain_id2pddA00
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology320 — Dihydrolipoamide Transferase
Homologous superfamily homologous superfamily10 — E3-binding domain
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8. Citations (1)

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9. Files and Curves (10)