SAXSdb — 3c4v

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

Predicted glycosyltransferases

Corynebacterium glutamicum

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	MAGNESIUM ION × 2 URIDINE-5'-DIPHOSPHATE × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	MAGNESIUM ION × 2 URIDINE-5'-DIPHOSPHATE × 2 L-MYO-INOSITOL-1-PHOSPHATE × 2 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 16	MAGNESIUM ION × 16 URIDINE-5'-DIPHOSPHATE × 16 L-MYO-INOSITOL-1-PHOSPHATE × 8 water × 16	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8NTA6_CORGL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–418； UniProt 1–418 Author chain B； PDBConstruct 1–418； UniProt 1–418

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	3c4v
Deposition date deposition_date	2008-01-30
Structure title title	Structure of the retaining glycosyltransferase MshA:The first step in mycothiol biosynthesis. Organism: Corynebacterium glutamicum : Complex with UDP and 1L-INS-1-P.
Keywords keywords	retaining glycosyltransferase, beta alpha beta, substrate assisted catalysis, TRANSFERASE; TRANSFERASE
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.

3c4v__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3c4v__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3c4v__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	78.81 Å
Rg (electron density)	78.15 Å
Total Rg	78.33 Å
Atom count	48952
Residues	6288
Excluded volume	863310 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3c4v__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3c4v__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3c4v__assembly_3__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	Predicted glycosyltransferases
Molecular weight formula_weight	46792.4 kDa
EC 编号 ec_number	2.4.1.-
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	6189

MRVAMISMHTSPLQQPGTGDSGGMNVYILSTATELAKQGIEVDIYTRATRPSQGEIVRVAENLRVINIAAGPYEGLSKEELPTQLAAFTGGMLSFTRREKVTYDLIHSHYWLSGQVGWLLRDLWRIPLIHTAHTLAAVKNSYRDDSDTPESEARRICEQQLVDNADVLAVNTQEEMQDLMHHYDADPDRISVVSPGADVELYSPGNDRATERSRRELGIPLHTKVVAFVGRLQPFKGPQVLIKAVAALFDRDPDRNLRVIICGGPSGPNATPDTYRHMAEELGVEKRIRFLDPRPPSELVAVYRAADIVAVPSFNESFGLVAMEAQASGTPVIAARVGGLPIAVAEGETGLLVDGHSPHAWADALATLLDDDETRIRMGEDAVEHARTFSWAATAAQLSSLYNDAIANENVDGETHHGLEHHHHHH

Source Source

Source organism organism	Corynebacterium glutamicum
NCBI taxonomy ID ncbi_taxonomy_id	1718
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	URIDINE-5'-DIPHOSPHATE
Molecular weight formula_weight	404.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	L-MYO-INOSITOL-1-PHOSPHATE
Molecular weight formula_weight	258.1 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	70

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3c4va_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.87 — UDP-Glycosyltransferase/glycogen phosphorylase
Superfamily Superfamily superfamily	c.87.1 — UDP-Glycosyltransferase/glycogen phosphorylase
Family Family family	c.87.1.0 — automated matches

Domain ID domain_id	d3c4vb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.87 — UDP-Glycosyltransferase/glycogen phosphorylase
Superfamily Superfamily superfamily	c.87.1 — UDP-Glycosyltransferase/glycogen phosphorylase
Family Family family	c.87.1.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id	3c4vA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2000 — Glycogen Phosphorylase B;

Domain ID domain_id	3c4vA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2000 — Glycogen Phosphorylase B;

Domain ID domain_id	3c4vB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2000 — Glycogen Phosphorylase B;

Domain ID domain_id	3c4vB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2000 — Glycogen Phosphorylase B;

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Unit-cell length a length_a	223.940 Å
Unit-cell length b length_b	223.940 Å
Unit-cell length c length_c	125.005 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	I 4 2 2
Space-group number int_tables_number	97
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	79.180 Å
R factor r_factor	0.1912
R_work r_work	0.1900
R_free r_free	0.2130

Structure of the retaining glycosyltransferase MshA:The first step in mycothiol biosynthesis. Organism: Corynebacterium glutamicum : Complex with UDP and 1L-INS-1-P.

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

Predicted glycosyltransferases

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

3c4v__assembly_3__model_1

3c4v__assembly_3__model_1 | I(q)

3c4v__assembly_3__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)

Structure of the retaining glycosyltransferase MshA:The first step in mycothiol biosynthesis. Organism: Corynebacterium glutamicum : Complex with UDP and 1L-INS-1-P.

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

Predicted glycosyltransferases

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

3c4v__assembly_3__model_1

3c4v__assembly_3__model_1 | I(q)

3c4v__assembly_3__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)