1ebd

DIHYDROLIPOAMIDE DEHYDROGENASE COMPLEXED WITH THE BINDING DOMAIN OF THE DIHYDROLIPOAMIDE ACETYLASE

Method: X-RAY DIFFRACTION D_max: 101.6 Å Quality: GOOD

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

DIHYDROLIPOAMIDE DEHYDROGENASE

Geobacillus stearothermophilus

UniProt P11959

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 7–461 Chain B； UniProt 7–461	Not recorded	DIHYDROLIPOAMIDE ACETYLTRANSFERASE × 1 （P11961） FAD FLAVIN-ADENINE DINUCLEOTIDE × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.60 Å

Other States of the Same Protein in the Database

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

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	DLD1_BACST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–455； UniProt 7–461 Author chain B； PDBConstruct 1–455； UniProt 7–461

DIHYDROLIPOAMIDE ACETYLTRANSFERASE

Geobacillus 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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain C； UniProt 129–169	Fragment：BINDING DOMAIN, RESIDUES 130 - 170	DIHYDROLIPOAMIDE DEHYDROGENASE × 2 （P11959） FAD FLAVIN-ADENINE DINUCLEOTIDE × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.60 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 1EBD	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
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 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 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 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 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 construct Different oligomeric state 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 construct Different oligomeric state 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 construct Different oligomeric state 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 construct Different oligomeric state 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 × 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 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 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 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 21 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ODP2_BACST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–41； UniProt 129–169

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	1ebd
Deposition date deposition_date	1996-02-03
Structure title title	DIHYDROLIPOAMIDE DEHYDROGENASE COMPLEXED WITH THE BINDING DOMAIN OF THE DIHYDROLIPOAMIDE ACETYLASE
Keywords keywords	REDOX-ACTIVE CENTER, GLYCOLYSIS, OXIDOREDUCTASE, COMPLEX (OXIDOREDUCTASE-TRANSFERASE) COMPLEX; 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	31.26 Å
Radius of gyration Rg (electron density) rg_electron	30.40 Å
Forward intensity I(0) i0	158198000.00
Molecular weight molecular_weight	101120.0 kDa
Excluded volume excluded_volume	127170 Å³
Envelope volume envelope_volume	154080 Å³
Hydration-shell volume shell_volume	42182 Å³
Envelope diameter envelope_diameter	107.3 Å
Shell Rg shell_rg	37.63 Å
Envelope Rg envelope_rg	30.46 Å
Shape Rg shape_rg	30.42 Å
Total Rg total_rg	30.95 Å
Total atoms total_atoms	7109
Residues n_residues	951
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	101.6 Å
Rg (real space) rg_real	31.22 Å
Rg uncertainty (real space) rg_real_error	0.62 Å
I(0) (real space) i0_real	1.5820e+08
I(0) uncertainty (real space) i0_real_error	2.1380e+06
Rg (reciprocal space) rg_reciprocal	31.24 Å
I(0) (reciprocal space) i0_reciprocal	158200000.0000
Solution quality estimate total_estimate	0.8930
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	37.9 Å
Skewness Skewness skewness	0.339
Kurtosis Kurtosis kurtosis	-0.308
Angular range angular_range	— – 0.2550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	44890000.0000
Real-space data points n_real_points	52
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.881; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.967

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	DIHYDROLIPOAMIDE DEHYDROGENASE
Molecular weight formula_weight	47795.4 kDa
EC 编号 ec_number	1.8.1.4
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	7146

AIETETLVVGAGPGGYVAAIRAAQLGQKVTIVEKGNLGGVCLNVGCIPSKALISASHRYEQAKHSEEMGIKAENVTIDFAKVQEWKASVVKKLTGGVEGLLKGNKVEIVKGEAYFVDANTVRVVNGDSAQTYTFKNAIIATGSRPIELPNFKFSNRILDSTGALNLGEVPKSLVVIGGGYIGIELGTAYANFGTKVTILEGAGEILSGFEKQMAAIIKKRLKKKGVEVVTNALAKGAEEREDGVTVTYEANGETKTIDADYVLVTVGRRPNTDELGLEQIGIKMTNRGLIEVDQQCRTSVPNIFAIGDIVPGPALAHKASYEGKVAAEAIAGHPSAVDYVAIPAVVFSDPECASVGYFEQQAKDEGIDVIAAKFPFAANGRALALNDTDGFLKLVVRKEDGVIIGAQIIGPNASDMIAELGLAIEAGMTAEDIALTIHAHPTLGEIAMEAAEVAL

来源 Source

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

Entity 2 Entity 2 polymer

Description description	DIHYDROLIPOAMIDE ACETYLTRANSFERASE
Molecular weight formula_weight	4438.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

IAMPSVRKYAREKGVDIRLVQGTGKNGRVLKEDIDAFLAGG

来源 Source

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

Entity 3 Entity 3 non-polymer

Description description	FLAVIN-ADENINE DINUCLEOTIDE
Molecular weight formula_weight	785.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	37

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7. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (7 domains)

Domain ID domain_id	d1ebda1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.3 — FAD/NAD(P)-binding domain
Superfamily Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
Family Family family	c.3.1.5 — FAD/NAD-linked reductases, N-terminal and central domains

Domain ID domain_id	d1ebda2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.3 — FAD/NAD(P)-binding domain
Superfamily Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
Family Family family	c.3.1.5 — FAD/NAD-linked reductases, N-terminal and central domains

Domain ID domain_id	d1ebda3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.87 — CO dehydrogenase flavoprotein C-domain-like
Superfamily Superfamily superfamily	d.87.1 — FAD/NAD-linked reductases, dimerisation (C-terminal) domain
Family Family family	d.87.1.1 — FAD/NAD-linked reductases, dimerisation (C-terminal) domain

Domain ID domain_id	d1ebdb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.3 — FAD/NAD(P)-binding domain
Superfamily Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
Family Family family	c.3.1.5 — FAD/NAD-linked reductases, N-terminal and central domains

Domain ID domain_id	d1ebdb2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.3 — FAD/NAD(P)-binding domain
Superfamily Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
Family Family family	c.3.1.5 — FAD/NAD-linked reductases, N-terminal and central domains

Domain ID domain_id	d1ebdb3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.87 — CO dehydrogenase flavoprotein C-domain-like
Superfamily Superfamily superfamily	d.87.1 — FAD/NAD-linked reductases, dimerisation (C-terminal) domain
Family Family family	d.87.1.1 — FAD/NAD-linked reductases, dimerisation (C-terminal) domain

Domain ID domain_id	d1ebdc_
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.9.1.1 — Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex

CATH v4.4 (7 domains)

Domain ID domain_id	1ebdA01
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

Domain ID domain_id	1ebdA02
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

Domain ID domain_id	1ebdA03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	390 — Enolase-like; domain 1
Homologous superfamily homologous superfamily	30 — FAD/NAD-linked reductase, C-terminal dimerisation domain

Domain ID domain_id	1ebdB01
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

Domain ID domain_id	1ebdB02
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

Domain ID domain_id	1ebdB03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	390 — Enolase-like; domain 1
Homologous superfamily homologous superfamily	30 — FAD/NAD-linked reductase, C-terminal dimerisation domain

Domain ID domain_id	1ebdC00
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	106.600 Å
Unit-cell length b length_b	106.600 Å
Unit-cell length c length_c	204.300 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.2150
R_work r_work	0.2150
R_free r_free	—

fit	/app/data/saxs_computation/eb/1ebd/1ebd.fit
pddf	/app/data/pr_computation/eb/1ebd/1ebd.pr.out
profile	/app/data/saxs_computation/eb/1ebd/1ebd.dat

DIHYDROLIPOAMIDE DEHYDROGENASE COMPLEXED WITH THE BINDING DOMAIN OF THE DIHYDROLIPOAMIDE ACETYLASE

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

DIHYDROLIPOAMIDE DEHYDROGENASE

State in the Current Structure

Other States of the Same Protein in the Database

DIHYDROLIPOAMIDE ACETYLTRANSFERASE

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

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (7 domains)

CATH v4.4 (7 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)