SAXSdb — 5ey8

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

Acyl-CoA synthase

Mycobacterium smegmatis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl icosyl hydrogen phosphate × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl icosyl hydrogen phosphate × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl icosyl hydrogen phosphate × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl icosyl hydrogen phosphate × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl icosyl hydrogen phosphate × 1 GLYCEROL × 1	Consistent with protein count
6	Protein monomer	Monomer	Protein 1	[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl icosyl hydrogen phosphate × 1 GLYCEROL × 1	Consistent with protein count
7	Protein monomer	Monomer	Protein 1	[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl icosyl hydrogen phosphate × 1	Consistent with protein count
8	Protein monomer	Monomer	Protein 1	[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl icosyl hydrogen phosphate × 1	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 Author chain B； PDBConstruct 1–630； UniProt 1–630 Author chain C； PDBConstruct 1–630； UniProt 1–630 Author chain D； PDBConstruct 1–630； UniProt 1–630 Author chain E； PDBConstruct 1–630； UniProt 1–630 Author chain F； PDBConstruct 1–630； UniProt 1–630 Author chain G； PDBConstruct 1–630； UniProt 1–630 Author chain H； PDBConstruct 1–630； UniProt 1–630

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	5ey8
Deposition date deposition_date	2015-11-24
Structure title title	Structure of FadD32 from Mycobacterium smegmatis complexed to AMPC20
Keywords keywords	Ligase, fatty-acyl AMP ligase; LIGASE
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.

5ey8__assembly_1__model_1

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

Download this curve (.dat)

5ey8__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5ey8__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.61 Å
Rg (electron density)	24.36 Å
Total Rg	25.20 Å
Atom count	4315
Residues	598
Excluded volume	75909 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5ey8__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5ey8__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`5ey8__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`5ey8__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`5ey8__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`5ey8__assembly_6__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`5ey8__assembly_7__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
8	1	`5ey8__assembly_8__model_1`	monomeric （1）	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 (3)

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	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	33378

MPFHNPFIKDGQIKFPDGSSIVAHVERWAKVRGDKLAYRFLDFSTERDGVPRDLTWAQFSARNRAVAARLQQVTQPGDRVAILCPQNLDYLVAFFGALYAGRIAVPLFDPSEPGHVGRLHAVLDNCHPSAILTTTEAAEGVRKFFRTRPANQRPRVIAVDAVPDDVASTWVNPDEPDETTIAYLQYTSGSTRIPTGVQITHLNLATNVVQVIEALEGEEGDRGLSWLPFFHDMGLITALLAPMIGHYFTFMTPAAFVRRPERWIRELARKEGDTGGTISVAPNFAFDHAAARGVPKPGSPPLDLSNVKAVLNGSEPISAATVRRFNEAFGPFGFPPKAIKPSYGLAEATLFVSTTPSAEEPKIITVDRDQLNSGRIVEVDADSPKAVAQASAGKVGIAEWAVIVDAESATELPDGQVGEIWISGQNMGTGYWGKPEESVATFQNILKSRTNPSHAEGATDDATWVRTGDYGAFYDGDLYITGRVKDLVIIDGRNHYPQDLEYSAQEASKAIRTGYVAAFSVPANQLPDEVFENAHSGIKRDPDDTSEQLVIVAERAPGAHKLDIGPITDDIRAAIAVRHGVTVRDVLLTAAGAIPRTSSGKIGRRACRAAYLDGSLRAGKVANDFPDATD

Source Source

Source organism organism	Mycobacterium smegmatis
NCBI taxonomy ID ncbi_taxonomy_id	1772
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl icosyl hydrogen phosphate
Molecular weight formula_weight	627.8 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 non-polymer

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

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6. Fold Classification (SCOP + CATH) 9 domains

CATH v4.4 (9 domains)

Domain ID domain_id	5ey8A01
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	5ey8B01
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	5ey8C01
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	5ey8D01
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	5ey8E01
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	5ey8F01
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	5ey8G01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	12780 — ANL, N-terminal domain

Domain ID domain_id	5ey8G02
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	5ey8H01
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

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Unit-cell length a length_a	164.040 Å
Unit-cell length b length_b	164.040 Å
Unit-cell length c length_c	231.530 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	32

Space group space_group	P 4
Space-group number int_tables_number	75
Crystal system crystal_system	—

Resolution resolution	3.500 Å
Low-resolution limit resolution_low	49.442 Å
R factor r_factor	0.2259
R_work r_work	0.2227
R_free r_free	0.2862

Structure of FadD32 from Mycobacterium smegmatis complexed to AMPC20

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5ey8__assembly_1__model_1

5ey8__assembly_1__model_1 | I(q)

5ey8__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 9 domains

CATH v4.4 (9 domains)

7. Citations (1)

Structure of FadD32 from Mycobacterium smegmatis complexed to AMPC20

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5ey8__assembly_1__model_1

5ey8__assembly_1__model_1 | I(q)

5ey8__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 9 domains

CATH v4.4 (9 domains)

7. Citations (1)