1v1r

CROSSTALK BETWEEN COFACTOR BINDING AND THE PHOSPHORYLATION LOOP CONFORMATION IN THE BCKD MACHINE

Method: X-RAY DIFFRACTION

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

2-OXOISOVALERATE DEHYDROGENASE ALPHA SUBUNIT

HOMO SAPIENS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	2-OXOISOVALERATE DEHYDROGENASE BETA SUBUNIT × 2 （P21953） CHLORIDE ION × 6 POTASSIUM ION × 4 SODIUM ION × 4 SULFATE ION × 2 GLYCEROL × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ODBA_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–400； UniProt 46–445

2-OXOISOVALERATE DEHYDROGENASE BETA SUBUNIT

HOMO SAPIENS

UniProt P21953

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	2-OXOISOVALERATE DEHYDROGENASE ALPHA SUBUNIT × 2 （P12694） CHLORIDE ION × 6 POTASSIUM ION × 4 SODIUM ION × 4 SULFATE ION × 2 GLYCEROL × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ODBB_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–342； UniProt 51–392

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	1v1r
Deposition date deposition_date	2004-04-22
Structure title title	CROSSTALK BETWEEN COFACTOR BINDING AND THE PHOSPHORYLATION LOOP CONFORMATION IN THE BCKD MACHINE
Keywords keywords	;OXIDOREDUCTASE, KETOACID DEHYDROGENASE, MULTI-ENZYME COMPLEX, ACYLATION, OXIDATIVE DECARBOXYLATION, MAPLE SYRUP URINE DISEASE, THIAMIN DIPHOSPHATE, PHOSPHORYLATION, FLAVOPROTEIN ;; 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.

1v1r__assembly_1__model_1

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

Download this curve (.dat)

1v1r__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1v1r__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	33.13 Å
Rg (electron density)	32.07 Å
Total Rg	32.76 Å
Atom count	10958
Residues	1376
Excluded volume	195110 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1v1r__assembly_1__model_1`	tetrameric （4）	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 (8)

Entity 1 Entity 1 polymer

Description description	2-OXOISOVALERATE DEHYDROGENASE ALPHA SUBUNIT
Molecular weight formula_weight	45504.0 kDa
EC 编号 ec_number	1.2.4.4
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	6170

SSLDDKPQFPGASAEFIDKLEFIQPNVISGIPIYRVMDRQGQIINPSEDPHLPKEKVLKLYKSMTLLNTMDRILYESQRQGRISFYMTNYGEEGTHVGSAAALDNTDLVFGQYREAGVLMYRDYPLELFMAQCYGNISDLGKGRQMPVHYGCKERHFVTISSPLATQIPQAVGAAYAAKRANANRVVICYFGEGAASEGDAHAGFNFAATLECPIIFFCRNNGYAISTPTSEQYRGDGIAARGPGYGIMSIRVDGNDVFAVYNATKEARRRAVAENQPFLIEAMTYRIGHASTSDDSSAYRSVDEVNYWDKQDHPISRLRHYLLSQGWWDEEQEKAWRKQSRRKVMEAFEQAERKPKPNPNLLFSDVYQEMPAQLRKQQESLARHLQTYGEHYPLDHFDK

Source Source

Source organism organism	HOMO SAPIENS
Common name common_name	HUMAN
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	2-OXOISOVALERATE DEHYDROGENASE BETA SUBUNIT
Molecular weight formula_weight	37902.3 kDa
EC 编号 ec_number	1.2.4.4
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

VAHFTFQPDPEPREYGQTQKMNLFQSVTSALDNSLAKDPTAVIFGEDVAFGGVFRCTVGLRDKYGKDRVFNTPLCEQGIVGFGIGIAVTGATAIAEIQFADYIFPAFDQIVNEAAKYRYRSGDLFNCGSLTIRSPWGCVGHGALYHSQSPEAFFAHCPGIKVVIPRSPFQAKGLLLSCIEDKNPCIFFEPKILYRAAAEEVPIEPYNIPLSQAEVIQEGSDVTLVAWGTQVHVIREVASMAKEKLGVSCEVIDLRTIIPWDVDTICKSVIKTGRLLISHEAPLTGGFASEISSTVQEECFLNLEAPISRVCGYDTPFPHIFEPFYIPDKWKCYDALRKMINY

Source Source

Source organism organism	HOMO SAPIENS
Common name common_name	HUMAN
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	ESCHERICHIA COLI

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

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

Entity 5 Entity 5 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	531

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1v1ra_
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	d1v1rb1
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.36.1.7 — Branched-chain alpha-keto acid dehydrogenase Pyr module

Domain ID domain_id	d1v1rb2
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.48.1.2 — Branched-chain alpha-keto acid dehydrogenase beta-subunit, C-terminal-domain

CATH v4.4 (3 domains)

Domain ID domain_id	1v1rA00
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	1v1rB01
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	1v1rB02
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

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Unit-cell length a length_a	145.135 Å
Unit-cell length b length_b	145.135 Å
Unit-cell length c length_c	69.226 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	6

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

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	23.770 Å
R factor r_factor	0.1580
R_work r_work	0.1570
R_free r_free	0.1830

CROSSTALK BETWEEN COFACTOR BINDING AND THE PHOSPHORYLATION LOOP CONFORMATION IN THE BCKD MACHINE

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

2-OXOISOVALERATE DEHYDROGENASE ALPHA SUBUNIT

State in the Current Structure

Other States of the Same Protein in the Database

2-OXOISOVALERATE DEHYDROGENASE BETA SUBUNIT

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

1v1r__assembly_1__model_1

1v1r__assembly_1__model_1 | I(q)

1v1r__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 (8)

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

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (4)

CROSSTALK BETWEEN COFACTOR BINDING AND THE PHOSPHORYLATION LOOP CONFORMATION IN THE BCKD MACHINE

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

2-OXOISOVALERATE DEHYDROGENASE ALPHA SUBUNIT

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-OXOISOVALERATE DEHYDROGENASE BETA SUBUNIT

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

1v1r__assembly_1__model_1

1v1r__assembly_1__model_1 | I(q)

1v1r__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 (8)

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

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (4)