6om8

Caenorhabditis Elegans UDP-Glucose Dehydrogenase in complex with UDP-Xylose

Method: X-RAY DIFFRACTION

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

UDP-glucose 6-dehydrogenase

Caenorhabditis elegans

UniProt Q19905

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	URIDINE-5'-DIPHOSPHATE-XYLOPYRANOSE × 12 water × 6	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 6	URIDINE-5'-DIPHOSPHATE-XYLOPYRANOSE × 12 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UGDH_CAEEL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–481； UniProt 1–481 Author chain B； PDBConstruct 1–481； UniProt 1–481 Author chain C； PDBConstruct 1–481； UniProt 1–481 Author chain D； PDBConstruct 1–481； UniProt 1–481 Author chain E； PDBConstruct 1–481； UniProt 1–481 Author chain F； PDBConstruct 1–481； UniProt 1–481 Author chain G； PDBConstruct 1–481； UniProt 1–481 Author chain H； PDBConstruct 1–481； UniProt 1–481 Author chain I； PDBConstruct 1–481； UniProt 1–481 Author chain J； PDBConstruct 1–481； UniProt 1–481 Author chain K； PDBConstruct 1–481； UniProt 1–481 Author chain L； PDBConstruct 1–481； UniProt 1–481

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	6om8
Deposition date deposition_date	2019-04-18
Structure title title	Caenorhabditis Elegans UDP-Glucose Dehydrogenase in complex with UDP-Xylose
Keywords keywords	Dehydrogenase, OXIDOREDUCTASE, OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex; OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR
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.

6om8__assembly_1__model_1

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

Download this curve (.dat)

6om8__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6om8__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	46.90 Å
Rg (electron density)	46.16 Å
Total Rg	46.44 Å
Atom count	21887
Residues	2783
Excluded volume	389590 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6om8__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6om8__assembly_2__model_1`	hexameric （6）	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	UDP-glucose 6-dehydrogenase
Molecular weight formula_weight	52812.0 kDa
EC 编号 ec_number	1.1.1.22
Source method src_method	man
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L
Atom count atom_count	44931

MTDQVFGKVSKVVCVGAGYVGGPTCAMIAHKCPHITVTVVDMNTAKIAEWNSDKLPIYEPGLDEIVFAARGRNLFFSSDIPKAIAEADLIFISVNTPTKMYGRGKGMAPDLKYVESVSRTIAQYAGGPKIVVEKSTVPVKAAESIGCILREAQKNNENLKFQVLSNPEFLAEGTAMKDLANPDRVLIGGESSPEGLQAVAELVRIYENWVPRNRIITTNTWSSELSKLVANAFLAQRISSINSISAVCEATGAEISEVAHAVGYDTRIGSKFLQASVGFGGSCFQKDVLSLVYLCESLNLPQVADYWQGVININNWQRRRFADKIIAELFNTVTDKKIAIFGFAFKKNTGDTRESSAIHVIKHLMEEHAKLSVYDPKVQKSQMLNDLASVTSAQDVERLITVESDPYAAARGAHAIVVLTEWDEFVELNYSQIHNDMQHPAAIFDGRLILDQKALREIGFRTFAIGTSPDQAYNLFGTAGY

Source Source

Source organism organism	Caenorhabditis elegans
NCBI taxonomy ID ncbi_taxonomy_id	6239
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	URIDINE-5'-DIPHOSPHATE-XYLOPYRANOSE
Molecular weight formula_weight	536.3 kDa
Source method src_method	syn
Copy count entity_count	24

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1194

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6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id	6om8A01
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	6om8B01
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	6om8C01
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	6om8D01
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	6om8E01
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	6om8F01
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	6om8G01
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	6om8H01
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	6om8I01
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	6om8J01
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	6om8K01
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	6om8L01
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

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Unit-cell length a length_a	157.710 Å
Unit-cell length b length_b	168.170 Å
Unit-cell length c length_c	279.560 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	48

Space group space_group	P 2 21 21
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.449 Å
Low-resolution limit resolution_low	52.698 Å
R factor r_factor	0.1937
R_work r_work	0.1935
R_free r_free	0.2204

Caenorhabditis Elegans UDP-Glucose Dehydrogenase in complex with UDP-Xylose

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

UDP-glucose 6-dehydrogenase

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

6om8__assembly_1__model_1

6om8__assembly_1__model_1 | I(q)

6om8__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 water

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)

Caenorhabditis Elegans UDP-Glucose Dehydrogenase in complex with UDP-Xylose

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

UDP-glucose 6-dehydrogenase

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

6om8__assembly_1__model_1

6om8__assembly_1__model_1 | I(q)

6om8__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 water

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)