SAXSdb — 2hdk

▼

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

Branched-chain-amino-acid aminotransferase, mitochondrial

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	PYRIDOXAL-5'-PHOSPHATE × 2 ACETIC ACID × 1 2-OXO-4-METHYLPENTANOIC ACID × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BCAT2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–365； UniProt 28–392 Author chain B； PDBConstruct 1–365； UniProt 28–392

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	2hdk
Deposition date deposition_date	2006-06-20
Structure title title	Crystal Structure of Cys315Ala-Cys318Ala Mutant of Human Mitochondrial Branched Chain Aminotransferase
Keywords keywords	D-aminoacid aminotransferase-like PLP-dependent enzymes, TRANSFERASE; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

2hdk__assembly_1__model_1

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

Download this curve (.dat)

2hdk__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2hdk__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.78 Å
Rg (electron density)	27.62 Å
Total Rg	28.44 Å
Atom count	5837
Residues	726
Excluded volume	104840 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2hdk__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Branched-chain-amino-acid aminotransferase, mitochondrial
Molecular weight formula_weight	41303.9 kDa
EC 编号 ec_number	2.6.1.42
Mutation mutation	C315A,C318A
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	5979

ASSSFKAADLQLEMTQKPHKKPGPGEPLVFGKTFTDHMLMVEWNDKGWGQPRIQPFQNLTLHPASSSLHYSLQLFEGMKAFKGKDQQVRLFRPWLNMDRMLRSAMRLCLPSFDKLELLECIRRLIEVDKDWVPDAAGTSLYVRPVLIGNEPSLGVSQPRRALLFVILCPVGAYFPGGSVTPVSLLADPAFIRAWVGGVGNYKLGGNYGPTVLVQQEALKRGCEQVLWLYGPDHQLTEVGTMNIFVYWTHEDGVLELVTPPLNGVILPGVVRQSLLDMAQTWGEFRVVERTITMKQLLRALEEGRVREVFGSGTAAQVAPVHRILYKDRNLHIPTMENGPELILRFQKELKEIQYGIRAHEWMFPV

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 BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	PYRIDOXAL-5'-PHOSPHATE
Molecular weight formula_weight	247.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	ACETIC ACID
Molecular weight formula_weight	60.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	2-OXO-4-METHYLPENTANOIC ACID
Molecular weight formula_weight	130.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	142

▼

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2hdka_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.17 — D-aminoacid aminotransferase-like PLP-dependent enzymes
Superfamily Superfamily superfamily	e.17.1 — D-aminoacid aminotransferase-like PLP-dependent enzymes
Family Family family	e.17.1.1 — D-aminoacid aminotransferase-like PLP-dependent enzymes

Domain ID domain_id	d2hdkb_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.17 — D-aminoacid aminotransferase-like PLP-dependent enzymes
Superfamily Superfamily superfamily	e.17.1 — D-aminoacid aminotransferase-like PLP-dependent enzymes
Family Family family	e.17.1.1 — D-aminoacid aminotransferase-like PLP-dependent enzymes

CATH v4.4 (4 domains)

Domain ID domain_id	2hdkA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	470 — D-amino Acid Aminotransferase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain

Domain ID domain_id	2hdkA02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	10 — D-amino Acid Aminotransferase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — D-amino Acid Aminotransferase, subunit A, domain 2

Domain ID domain_id	2hdkB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	470 — D-amino Acid Aminotransferase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain

Domain ID domain_id	2hdkB02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	10 — D-amino Acid Aminotransferase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — D-amino Acid Aminotransferase, subunit A, domain 2

▶

Unit-cell length a length_a	59.480 Å
Unit-cell length b length_b	112.187 Å
Unit-cell length c length_c	60.265 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	96.16 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	25.000 Å
R factor r_factor	0.3200
R_work r_work	0.1820
R_free r_free	0.2370

Crystal Structure of Cys315Ala-Cys318Ala Mutant of Human Mitochondrial Branched Chain Aminotransferase

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

Branched-chain-amino-acid aminotransferase, mitochondrial

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

2hdk__assembly_1__model_1

2hdk__assembly_1__model_1 | I(q)

2hdk__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal Structure of Cys315Ala-Cys318Ala Mutant of Human Mitochondrial Branched Chain Aminotransferase

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

Branched-chain-amino-acid aminotransferase, mitochondrial

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

2hdk__assembly_1__model_1

2hdk__assembly_1__model_1 | I(q)

2hdk__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)