2x6t

AGME bound to ADP-B-mannose

Method: X-RAY DIFFRACTION

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

ADP-L-GLYCERO-D-MANNO-HEPTOSE-6-EPIMERASE

ESCHERICHIA COLI

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 GLYCEROL × 1 ADENOSINE-5'-DIPHOSPHATE × 1 beta-D-mannopyranose × 1 water × 1	Consistent with protein count
10	Protein monomer	Monomer	Protein 1	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 GLYCEROL × 1 ADENOSINE-5'-DIPHOSPHATE × 1 beta-D-mannopyranose × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 GLYCEROL × 1 ADENOSINE-5'-DIPHOSPHATE × 1 beta-D-mannopyranose × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 GLYCEROL × 1 ADENOSINE-5'-DIPHOSPHATE × 1 beta-D-mannopyranose × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 GLYCEROL × 1 ADENOSINE-5'-DIPHOSPHATE × 1 beta-D-mannopyranose × 1 water × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 GLYCEROL × 1 ADENOSINE-5'-DIPHOSPHATE × 1 beta-D-mannopyranose × 1 water × 1	Consistent with protein count
6	Protein monomer	Monomer	Protein 1	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 GLYCEROL × 1 ADENOSINE-5'-DIPHOSPHATE × 1 beta-D-mannopyranose × 1 water × 1	Consistent with protein count
7	Protein monomer	Monomer	Protein 1	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 GLYCEROL × 1 ADENOSINE-5'-DIPHOSPHATE × 1 beta-D-mannopyranose × 1 CHLORIDE ION × 2 water × 1	Consistent with protein count
8	Protein monomer	Monomer	Protein 1	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 GLYCEROL × 1 ADENOSINE-5'-DIPHOSPHATE × 1 beta-D-mannopyranose × 1 water × 1	Consistent with protein count
9	Protein monomer	Monomer	Protein 1	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 GLYCEROL × 1 ADENOSINE-5'-DIPHOSPHATE × 1 beta-D-mannopyranose × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HLDD_ECO57
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 48–357； UniProt 1–310 Author chain B； PDBConstruct 48–357； UniProt 1–310 Author chain C； PDBConstruct 48–357； UniProt 1–310 Author chain D； PDBConstruct 48–357； UniProt 1–310 Author chain E； PDBConstruct 48–357； UniProt 1–310 Author chain F； PDBConstruct 48–357； UniProt 1–310 Author chain G； PDBConstruct 48–357； UniProt 1–310 Author chain H； PDBConstruct 48–357； UniProt 1–310 Author chain I； PDBConstruct 48–357； UniProt 1–310 Author chain J； PDBConstruct 48–357； UniProt 1–310

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	2x6t
Deposition date deposition_date	2010-02-21
Structure title title	AGME bound to ADP-B-mannose
Keywords keywords	ISOMERASE, CARBOHYDRATE METABOLISM, STRESS RESPONSE; 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.

2x6t__assembly_3__model_1

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

Download this curve (.dat)

2x6t__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2x6t__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	19.59 Å
Rg (electron density)	18.65 Å
Total Rg	19.55 Å
Atom count	2532
Residues	307
Excluded volume	44620 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2x6t__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2x6t__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2x6t__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2x6t__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`2x6t__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`2x6t__assembly_6__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`2x6t__assembly_7__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
8	1	`2x6t__assembly_8__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
9	1	`2x6t__assembly_9__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
10	1	`2x6t__assembly_10__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 (7)

Entity 1 Entity 1 polymer

Description description	ADP-L-GLYCERO-D-MANNO-HEPTOSE-6-EPIMERASE
Molecular weight formula_weight	39891.5 kDa
EC 编号 ec_number	5.1.3.20
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	10

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J
Atom count atom_count	26879

MHHHHHHSSGLVPRGSGMKETAAAKFERQHMDSPDLGTGGGSGIEGRMIIVTGGAGFIGSNIVKALNDKGITDILVVDNLKDGTKFVNLVDLNIADYMDKEDFLIQIMAGEEFGDVEAIFHEGACSSTTEWDGKYMMDNNYQYSKELLHYCLEREIPFLYASSAATYGGRTSDFIESREYEKPLNVFGYSKFLFDEYVRQILPEANSQIVGFRYFNVYGPREGHKGSMASVAFHLNTQLNNGESPKLFEGSENFKRDFVYVGDVADVNLWFLENGVSGIFNLGTGRAESFQAVADATLAYHKKGQIEYIPFPDKLKGRYQAFTQADLTNLRAAGYDKPFKTVAEGVTEYMAWLNRDA

Source Source

Source organism organism	ESCHERICHIA COLI
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Molecular weight formula_weight	743.4 kDa
Source method src_method	syn
Copy count entity_count	10

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	10

Entity 4 Entity 4 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 5 Entity 5 non-polymer

Description description	beta-D-mannopyranose
Molecular weight formula_weight	180.2 kDa
Source method src_method	man
Copy count entity_count	10

Entity 6 Entity 6 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1546

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6. Fold Classification (SCOP + CATH) 30 domains

SCOP 2.08 (10 domains)

Domain ID domain_id	d2x6ta_
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	d2x6tb_
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	d2x6tc_
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	d2x6td_
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	d2x6te_
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	d2x6tf_
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	d2x6tg_
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	d2x6th_
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	d2x6ti_
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	d2x6tj_
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 (20 domains)

Domain ID domain_id	2x6tA01
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	2x6tA02
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	2x6tB01
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	2x6tB02
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	2x6tC01
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	2x6tC02
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	2x6tD01
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	2x6tD02
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	2x6tE01
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	2x6tE02
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	2x6tF01
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	2x6tF02
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	2x6tG01
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	2x6tG02
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	2x6tH01
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	2x6tH02
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	2x6tI01
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	2x6tI02
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	2x6tJ01
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	2x6tJ02
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	341.993 Å
Unit-cell length b length_b	60.787 Å
Unit-cell length c length_c	191.789 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.41 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	40

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.360 Å
Low-resolution limit resolution_low	38.690 Å
R factor r_factor	0.1903
R_work r_work	0.1893
R_free r_free	0.2089

AGME bound to ADP-B-mannose

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

ADP-L-GLYCERO-D-MANNO-HEPTOSE-6-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

2x6t__assembly_3__model_1

2x6t__assembly_3__model_1 | I(q)

2x6t__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 (7)

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 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 30 domains

SCOP 2.08 (10 domains)

CATH v4.4 (20 domains)

7. Citations (1)

AGME bound to ADP-B-mannose

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

ADP-L-GLYCERO-D-MANNO-HEPTOSE-6-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

2x6t__assembly_3__model_1

2x6t__assembly_3__model_1 | I(q)

2x6t__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 (7)

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 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 30 domains

SCOP 2.08 (10 domains)

CATH v4.4 (20 domains)

7. Citations (1)