SAXSdb — 3wyj

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

Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)

Escherichia coli K-12

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	;[1-oxidanyl-2-[3-[3-[[3-[[3-[3-(2-oxidanyl-2,2-diphosphono-ethyl)phenyl]phenyl]sulfamoyl]phenyl]sulfonylamino]phenyl]phenyl]-1-phosphono-ethyl]phosphonic acid ; × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UPPS_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–253； UniProt 1–253 Author chain B； PDBConstruct 1–253； UniProt 1–253

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	3wyj
Deposition date deposition_date	2014-08-29
Structure title title	Structure of E. coli undecaprenyl diphosphate synthase in complex with BPH-789
Keywords keywords	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.

3wyj__assembly_1__model_1

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

Download this curve (.dat)

3wyj__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3wyj__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.70 Å
Rg (electron density)	23.52 Å
Total Rg	24.46 Å
Atom count	3563
Residues	441
Excluded volume	62645 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3wyj__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 (3)

Entity 1 Entity 1 polymer

Description description	Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)
Molecular weight formula_weight	28481.1 kDa
EC 编号 ec_number	2.5.1.31
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	3988

MMLSATQPLSEKLPAHGCRHVAIIMDGNGRWAKKQGKIRAFGHKAGAKSVRRAVSFAANNGIEALTLYAFSSENWNRPAQEVSALMELFVWALDSEVKSLHRHNVRLRIIGDTSRFNSRLQERIRKSEALTAGNTGLTLNIAANYGGRWDIVQGVRQLAEKVQQGNLQPDQIDEEMLNQHVCMHELAPVDLVIRTGGEHRISNFLLWQIAYAELYFTDVLWPDFDEQDFEGALNAFANRERRFGGTEPGDETA

Source Source

Source organism organism	Escherichia coli K-12
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	;[1-oxidanyl-2-[3-[3-[[3-[[3-[3-(2-oxidanyl-2,2-diphosphono-ethyl)phenyl]phenyl]sulfamoyl]phenyl]sulfonylamino]phenyl]phenyl]-1-phosphono-ethyl]phosphonic acid ;
Molecular weight formula_weight	948.7 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	425

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3wyja_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.101 — Undecaprenyl diphosphate synthase
Superfamily Superfamily superfamily	c.101.1 — Undecaprenyl diphosphate synthase
Family Family family	c.101.1.1 — Undecaprenyl diphosphate synthase

Domain ID domain_id	d3wyjb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.101 — Undecaprenyl diphosphate synthase
Superfamily Superfamily superfamily	c.101.1 — Undecaprenyl diphosphate synthase
Family Family family	c.101.1.1 — Undecaprenyl diphosphate synthase

CATH v4.4 (2 domains)

Domain ID domain_id	3wyjA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1180 — Undecaprenyl pyrophosphate synthetase
Homologous superfamily homologous superfamily	10 — Decaprenyl diphosphate synthase-like

Domain ID domain_id	3wyjB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1180 — Undecaprenyl pyrophosphate synthetase
Homologous superfamily homologous superfamily	10 — Decaprenyl diphosphate synthase-like

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Unit-cell length a length_a	63.712 Å
Unit-cell length b length_b	68.995 Å
Unit-cell length c length_c	108.885 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	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	25.000 Å
R factor r_factor	—
R_work r_work	0.2000
R_free r_free	0.2410

Structure of E. coli undecaprenyl diphosphate synthase in complex with BPH-789

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

Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)

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

3wyj__assembly_1__model_1

3wyj__assembly_1__model_1 | I(q)

3wyj__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Structure of E. coli undecaprenyl diphosphate synthase in complex with BPH-789

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

Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)

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

3wyj__assembly_1__model_1

3wyj__assembly_1__model_1 | I(q)

3wyj__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)