SAXSdb — 2c5a

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

;GDP-MANNOSE-3', 5'-EPIMERASE ;

Arabidopsis thaliana

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	GUANOSINE-5'-DIPHOSPHATE-BETA-L-GALACTOSE × 2 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 FORMIC ACID × 17 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GMANE_ARATH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–379； UniProt 1–377 Author chain B； PDBConstruct 3–379； UniProt 1–377

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	2c5a
Deposition date deposition_date	2005-10-26
Structure title title	GDP-mannose-3', 5' -epimerase (Arabidopsis thaliana),Y174F, with GDP-beta-L-galactose bound in the active site
Keywords keywords	;3' 5'-EPIMERASE, SHORT CHAIN DEHYDRATASE/REDUCTASE, GDP-MANNOSE, GDP-GULOSE, GDP-GALACTOSE, KETO INTERMEDIATE, VITAMIN C, SDR, ASCORBATE BIOSYNTHESIS, ISOMERASE, NAD ;; ISOMERASE
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.

2c5a__assembly_1__model_1

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

Download this curve (.dat)

2c5a__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2c5a__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.29 Å
Rg (electron density)	27.69 Å
Total Rg	28.33 Å
Atom count	6017
Residues	725
Excluded volume	105910 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2c5a__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 (6)

Entity 1 Entity 1 polymer

Description description	;GDP-MANNOSE-3', 5'-EPIMERASE ;
Molecular weight formula_weight	42927.6 kDa
EC 编号 ec_number	5.1.3.18
Mutation mutation	YES
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	7235

GAMGTTNGTDYGAYTYKELEREQYWPSENLKISITGAGGFIASHIARRLKHEGHYVIASDWKKNEHMTEDMFCDEFHLVDLRVMENCLKVTEGVDHVFNLAADMGGMGFIQSNHSVIMYNNTMISFNMIEAARINGIKRFFYASSACIYPEFKQLETTNVSLKESDAWPAEPQDAFGLEKLATEELCKHYNKDFGIECRIGRFHNIYGPFGTWKGGREKAPAAFCRKAQTSTDRFEMWGDGLQTRSFTFIDECVEGVLRLTKSDFREPVNIGSDEMVSMNEMAEMVLSFEEKKLPIHHIPGPEGVRGRNSDNNLIKEKLGWAPNMRLKEGLRITYFWIKEQIEKEKAKGSDVSLYGSSKVVGTQAPVQLGSLRAADGKE

Source Source

Source organism organism	Arabidopsis thaliana
Common name common_name	MOUSE-EAR CRESS
NCBI taxonomy ID ncbi_taxonomy_id	3702
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	GUANOSINE-5'-DIPHOSPHATE-BETA-L-GALACTOSE
Molecular weight formula_weight	605.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Molecular weight formula_weight	663.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	FORMIC ACID
Molecular weight formula_weight	46.0 kDa
Source method src_method	syn
Copy count entity_count	17

Entity 5 Entity 5 non-polymer

Description description	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Molecular weight formula_weight	209.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1018

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2c5aa1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.2 — Tyrosine-dependent oxidoreductases

Domain ID domain_id	d2c5ab_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.2 — Tyrosine-dependent oxidoreductases

CATH v4.4 (4 domains)

Domain ID domain_id	2c5aA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	2c5aA02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	25 — UDP-galactose 4-epimerase; domain 1
Homologous superfamily homologous superfamily	10 — UDP-galactose 4-epimerase, domain 1

Domain ID domain_id	2c5aB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	2c5aB02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	25 — UDP-galactose 4-epimerase; domain 1
Homologous superfamily homologous superfamily	10 — UDP-galactose 4-epimerase, domain 1

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Unit-cell length a length_a	62.497 Å
Unit-cell length b length_b	83.273 Å
Unit-cell length c length_c	66.120 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	98.89 °
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	1.400 Å
Low-resolution limit resolution_low	21.610 Å
R factor r_factor	0.1050
R_work r_work	0.1030
R_free r_free	0.1400

GDP-mannose-3', 5' -epimerase (Arabidopsis thaliana),Y174F, with GDP-beta-L-galactose bound in the active site

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

;GDP-MANNOSE-3', 5'-EPIMERASE ;

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

2c5a__assembly_1__model_1

2c5a__assembly_1__model_1 | I(q)

2c5a__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 (6)

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 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)

GDP-mannose-3', 5' -epimerase (Arabidopsis thaliana),Y174F, with GDP-beta-L-galactose bound in the active site

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

;GDP-MANNOSE-3', 5'-EPIMERASE ;

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

2c5a__assembly_1__model_1

2c5a__assembly_1__model_1 | I(q)

2c5a__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 (6)

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 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)