SAXSdb — 5d6j

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

Acyl-CoA synthase

Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Ubiquitin-like protein SMT3 × 1 （Q12306） MAGNESIUM ION × 1 ADENOSINE-5'-TRIPHOSPHATE × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0R618_MYCS2
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–630； UniProt 1–630

Ubiquitin-like protein SMT3

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt Q12306

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Acyl-CoA synthase × 1 （A0R618） MAGNESIUM ION × 1 ADENOSINE-5'-TRIPHOSPHATE × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SMT3_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–74； UniProt 21–94

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	5d6j
Deposition date deposition_date	2015-08-12
Structure title title	Crystal structure of a mycobacterial protein
Keywords keywords	Mycobacterium smegmatis, LIGASE-PROTEIN BINDING complex; LIGASE/PROTEIN BINDING
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.

5d6j__assembly_1__model_1

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

Download this curve (.dat)

5d6j__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5d6j__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.53 Å
Rg (electron density)	27.56 Å
Total Rg	28.33 Å
Atom count	5461
Residues	704
Excluded volume	96175 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5d6j__assembly_1__model_1`	dimeric （2）	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	Acyl-CoA synthase
Molecular weight formula_weight	68306.5 kDa
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	5943

MPFHNPFIKDGQIKFPDGSSIVAHVERWAKVRGDKLAYRFLDFSTERDGVPRDLTWAQFSARNRAVAARLQQVTQPGDRVAILCPQNLDYLVAFFGALYAGRIAVPLFDPSEPGHVGRLHAVLDNCHPSAILTTTEAAEGVRKFFRTRPANQRPRVIAVDAVPDDVASTWVNPDEPDETTIAYLQYTSGSTRIPTGVQITHLNLATNVVQVIEALEGEEGDRGLSWLPFFHDMGLITALLAPMIGHYFTFMTPAAFVRRPERWIRELARKEGDTGGTISVAPNFAFDHAAARGVPKPGSPPLDLSNVKAVLNGSEPISAATVRRFNEAFGPFGFPPKAIKPSYGLAEATLFVSTTPSAEEPKIITVDRDQLNSGRIVEVDADSPKAVAQASAGKVGIAEWAVIVDAESATELPDGQVGEIWISGQNMGTGYWGKPEESVATFQNILKSRTNPSHAEGATDDATWVRTGDYGAFYDGDLYITGRVKDLVIIDGRNHYPQDLEYSAQEASKAIRTGYVAAFSVPANQLPDEVFENAHSGIKRDPDDTSEQLVIVAERAPGAHKLDIGPITDDIRAAIAVRHGVTVRDVLLTAAGAIPRTSSGKIGRRACRAAYLDGSLRAGKVANDFPDATD

Source Source

Source organism organism	Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
NCBI taxonomy ID ncbi_taxonomy_id	246196
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Ubiquitin-like protein SMT3
Molecular weight formula_weight	8696.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

ETHINLKVSDGSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHRE

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli

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	1

Entity 4 Entity 4 non-polymer

Description description	ADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 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	482

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6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d5d6jb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.1 — Ubiquitin-related

CATH v4.4 (2 domains)

Domain ID domain_id	5d6jA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	300 — GMP Synthetase; Chain A, domain 3
Homologous superfamily homologous superfamily	30 — ANL, C-terminal domain

Domain ID domain_id	5d6jB00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

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Unit-cell length a length_a	122.211 Å
Unit-cell length b length_b	122.211 Å
Unit-cell length c length_c	142.588 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.250 Å
Low-resolution limit resolution_low	29.985 Å
R factor r_factor	0.1702
R_work r_work	0.1688
R_free r_free	0.2062

Crystal structure of a mycobacterial protein

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

Acyl-CoA synthase

State in the Current Structure

Other States of the Same Protein in the Database

Ubiquitin-like protein SMT3

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

5d6j__assembly_1__model_1

5d6j__assembly_1__model_1 | I(q)

5d6j__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 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of a mycobacterial protein

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

Acyl-CoA synthase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ubiquitin-like protein SMT3

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

5d6j__assembly_1__model_1

5d6j__assembly_1__model_1 | I(q)

5d6j__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 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

7. Citations (1)