SAXSdb — 8p5r

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

Multifunctional 2-oxoglutarate metabolism enzyme

Mycolicibacterium smegmatis MC2 155

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 16	Glycogen accumulation regulator GarA × 6 （A0QYG2） MAGNESIUM ION × 6 CALCIUM ION × 8 THIAMINE DIPHOSPHATE × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	KGD_MYCS2
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 25–1250； UniProt 2–1227 Author chain B； PDBConstruct 25–1250； UniProt 2–1227 Author chain C； PDBConstruct 25–1250； UniProt 2–1227 Author chain D； PDBConstruct 25–1250； UniProt 2–1227 Author chain E； PDBConstruct 25–1250； UniProt 2–1227 Author chain F； PDBConstruct 25–1250； UniProt 2–1227 Author chain N； PDBConstruct 25–1250； UniProt 2–1227 Author chain O； PDBConstruct 25–1250； UniProt 2–1227 Author chain P； PDBConstruct 25–1250； UniProt 2–1227 Author chain Q； PDBConstruct 25–1250； UniProt 2–1227

Glycogen accumulation regulator GarA

Mycolicibacterium smegmatis MC2 155

UniProt A0QYG2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 16	Multifunctional 2-oxoglutarate metabolism enzyme × 10 （A0R2B1） MAGNESIUM ION × 6 CALCIUM ION × 8 THIAMINE DIPHOSPHATE × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GARA_MYCS2
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain G； PDBConstruct 1–158； UniProt 1–158 Author chain H； PDBConstruct 1–158； UniProt 1–158 Author chain I； PDBConstruct 1–158； UniProt 1–158 Author chain J； PDBConstruct 1–158； UniProt 1–158 Author chain K； PDBConstruct 1–158； UniProt 1–158 Author chain L； PDBConstruct 1–158； UniProt 1–158

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8p5r
Deposition date deposition_date	2023-05-24
Structure title title	Crystal structure of full-length, homohexameric 2-oxoglutarate dehydrogenase KGD from Mycobacterium smegmatis in complex with GarA
Keywords keywords	2-oxoglutarate dehydrogenase; ODH; KGD; OXIDOREDUCTASE, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

8p5r__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

8p5r__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8p5r__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	71.35 Å
Rg (electron density)	71.04 Å
Total Rg	71.06 Å
Atom count	57005
Residues	7346
Excluded volume	1006200 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8p5r__assembly_1__model_1`	hexadecameric （16）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Multifunctional 2-oxoglutarate metabolism enzyme
Molecular weight formula_weight	138548.1 kDa
EC 编号 ec_number	2.2.1.5,4.1.1.71,1.2.4.2,2.3.1.61
Source method src_method	man
Copy count entity_count	10

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,N,O,P,Q
Atom count atom_count	57005

MGSSHHHHHHSSGLVPRGSHMASVSSSPSPFGQNEWLVEEMYRKFRDDPSSVDPSWHEFLVDYSPEPTTDSASNGRTTTAAPVTPPTPAPAPAPEPKAAPKPAAKTEAKPAKPAKSATPAKGDESQILRGAAAAVVKNMNASLEVPTATSVRAIPAKLMIDNRVVINNHLKRTRGGKISFTHLLGYAIVQAVKKFPNMNRHFAVVDGKPTAITPAHTNLGLAIDLQGKDGNRSLVVAAIKRCETMRFGQFIAAYEDIVRRARDGKLTAEDFSGVTISLTNPGTLGTVHSVPRLMQGQGAIIGAGAMEYPAEFQGASEERIADLGIGKLITLTSTYDHRIIQGAESGDFLRTIHQLLLDDDFFDEIFRELGIPYEPVRWRTDNPDSIEDKNARVIELIAAYRNRGHLMADIDPLRLDNTRFRSHPDLDVNSHGLTLWDLDREFKVDGFAGVQRKKLRDILSVLRDAYCRHVGVEYTHILEPEQQRWIQERVETKHDKPTVAEQKYILSKLNAAEAFETFLQTKYVGQKRFSLEGAETVIPMMDAVIDQCAEHGLDEVVIAMPHRGRLNVLANIVGKPYSQIFSEFEGNLNPSQAHGSGDVKYHLGATGTYIQMFGDNDIEVSLTANPSHLEAVDPVLEGLVRAKQDLLDTGEEGSDNRFSVVPLMLHGDAAFAGQGVVAETLNLALLRGYRTGGTIHIVVNNQIGFTTAPTDSRSSEYCTDVAKMIGAPIFHVNGDDPEACAWVARLAVDFRQAFKKDVVIDMLCYRRRGHNEGDDPSMTQPYMYDVIDTKRGSRKAYTEALIGRGDISMKEAEDALRDYQGQLERVFNEVRELEKHEIEPSESVEADQQIPSKLATAVDKAMLQRIGDAHLALPEGFTVHPRVRPVLEKRREMAYEGRIDWAFAELLALGSLIAEGKLVRLSGQDTQRGTFTQRHAVIVDRKTGEEFTPLQLLATNPDGTPTGGKFLVYNSALSEFAAVGFEYGYSVGNPDAMVLWEAQFGDFVNGAQSIIDEFISSGEAKWGQLSDVVLLLPHGHEGQGPDHTSGRIERFLQLWAEGSMTIAMPSTPANYFHLLRRHGKDGIQRPLIVFTPKSMLRNKAAVSDIRDFTESKFRSVLEEPMYTDGEGDRNKVTRLLLTSGKIYYELAARKAKENREDVAIVRIEQLAPLPRRRLAETLDRYPNVKEKFWVQEEPANQGAWPSFGLTLPEILPDHFTGLKRISRRAMSAPSSGSSKVHAVEQQEILDTAFG

Source Source

Source organism organism	Mycolicibacterium smegmatis MC2 155
NCBI taxonomy ID ncbi_taxonomy_id	246196
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Glycogen accumulation regulator GarA
Molecular weight formula_weight	16599.0 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

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

MTDKDSNLGADQSEDVTVETTSVFRADFLNELDAPAAAGTEGAVSGVEGLPSGSALLVVKRGPNAGSRFLLDQPTTSAGRHPDSDIFLDDVTVSRRHAEFRLEGGEFQVVDVGSLNGTYVNREPVDSAVLANGDEVQIGKFRLVFLTGPKSDDSGSNA

Source Source

Source organism organism	Mycolicibacterium smegmatis MC2 155
NCBI taxonomy ID ncbi_taxonomy_id	246196
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 non-polymer

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

Entity 4 Entity 4 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 5 Entity 5 non-polymer

Description description	THIAMINE DIPHOSPHATE
Molecular weight formula_weight	425.3 kDa
Source method src_method	syn
Copy count entity_count	6

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Unit-cell length a length_a	325.750 Å
Unit-cell length b length_b	325.750 Å
Unit-cell length c length_c	396.944 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	60

Space group space_group	P 65
Space-group number int_tables_number	170
Crystal system crystal_system	—

Resolution resolution	4.562 Å
Low-resolution limit resolution_low	45.990 Å
R factor r_factor	0.1998
R_work r_work	0.1983
R_free r_free	0.2292

Crystal structure of full-length, homohexameric 2-oxoglutarate dehydrogenase KGD from Mycobacterium smegmatis in complex with GarA

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

Multifunctional 2-oxoglutarate metabolism enzyme

State in the Current Structure

Other States of the Same Protein in the Database

Glycogen accumulation regulator GarA

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8p5r__assembly_1__model_1

8p5r__assembly_1__model_1 | I(q)

8p5r__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

7. Citations (2)

Crystal structure of full-length, homohexameric 2-oxoglutarate dehydrogenase KGD from Mycobacterium smegmatis in complex with GarA

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

Multifunctional 2-oxoglutarate metabolism enzyme

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Glycogen accumulation regulator GarA

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8p5r__assembly_1__model_1

8p5r__assembly_1__model_1 | I(q)

8p5r__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

7. Citations (2)