SAXSdb — 5ubk

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

Acyl-homoserine lactone acylase PvdQ

Pseudomonas aeruginosa

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	;N-[(1R)-1-{(6S)-6-[(2-amino-2-oxoethyl)carbamoyl]-1,4,5,6-tetrahydropyrimidin-2-yl}-2-(4-hydroxyphenyl)ethyl]-N~2~-tetradecanoyl-L-glutamine ; × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PVDQ_PSEAE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–546； UniProt 217–762 Author chain A； PDBConstruct 548–709； UniProt 30–191

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	5ubk
Deposition date deposition_date	2016-12-20
Structure title title	Inactive S1A/N269D-cpPvdQ mutant in complex with the pyoverdine precursor PVDIq reveals a specific binding pocket for the D-Tyr of this substrate
Keywords keywords	cpPVDQ, cpPVDQ S1A/269D, pyoverdine precursor, substrate:mutant PVDQ complex, HYDROLASE; HYDROLASE
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.

5ubk__assembly_1__model_1

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

Download this curve (.dat)

5ubk__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5ubk__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.39 Å
Rg (electron density)	26.08 Å
Total Rg	26.99 Å
Atom count	5540
Residues	709
Excluded volume	97636 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5ubk__assembly_1__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 (3)

Entity 1 Entity 1 polymer

Description description	Acyl-homoserine lactone acylase PvdQ
Molecular weight formula_weight	78179.8 kDa
EC 编号 ec_number	3.5.1.97
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	5695

ANAIAVGSERSADGKGMLLANPHFPWNGAMRFYQMHLTIPGRLDVMGASLPGLPVVNIGFSRHLAWTHTVDTSSHFTLYRLALDPKDPRRYLVDGRSLPLEEKSVAIEVRGADGKLSRVEHKVYQSIYGPLVVWPGKLDWNRSEAYALRDANLENTRVLQQWYSINQASDVADLRRRVEALQGIPWVNTLAADEQGNALYMNQSVVPYLKPELIPACAIPQLVAEGLPALQGQDSRCAWSRDPAAAQAGITPAAQLPVLLRRDFVQNSDDSAWLTNPASPLQGFSPLVSQEKPIGPRARYALSRLQGKQPLEAKTLEEMVTANHVFSADQVLPDLLRLCRDNQGEKSLARACAALAQWDRGANLDSGSGFVYFQRFMQRFAELDGAWKEPFDAQRPLDTPQGIALDRPQVATQVRQALADAAAEVEKSGIPDGARWGDLQVSTRGQERIAIPGGDGHFGVYNAIQSVRKGDHLEVVGGTSYIQLVTFPEEGPKARGLLAFSQSSDPRSPHYRDQTELFSRQQWQTLPFSDRQIDADPQLQRLSIREGGLAADIRWTAYGVPHIRAKDERGLGYGIGYAYARDNACLLAEEIVTARGERARYFGSEGKSSAELDNLPSDIFYAWLNQPEALQAFWQAQTPAVRQLLEGYAAGFNRFLREADGKTTSCLGQPWLRAIATDDLLRLTRRLLVEGGVGQFADALVAAAPPGAE

Source Source

Source organism organism	Pseudomonas aeruginosa
NCBI taxonomy ID ncbi_taxonomy_id	287
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	;N-[(1R)-1-{(6S)-6-[(2-amino-2-oxoethyl)carbamoyl]-1,4,5,6-tetrahydropyrimidin-2-yl}-2-(4-hydroxyphenyl)ethyl]-N~2~-tetradecanoyl-L-glutamine ;
Molecular weight formula_weight	658.8 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	152

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	5ubkA01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	120 — Penicillin G acylase, beta-roll domain
Homologous superfamily homologous superfamily	10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain, beta-sheet knob region

Domain ID domain_id	5ubkA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1400 — Penicillin amidase (Acylase) alpha subunit, N-terminal domain
Homologous superfamily homologous superfamily	10 — Aminohydrolase, alpha-helical knob region

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Unit-cell length a length_a	120.384 Å
Unit-cell length b length_b	168.361 Å
Unit-cell length c length_c	93.643 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	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.550 Å
Low-resolution limit resolution_low	39.035 Å
R factor r_factor	0.1871
R_work r_work	0.1844
R_free r_free	0.2369

Inactive S1A/N269D-cpPvdQ mutant in complex with the pyoverdine precursor PVDIq reveals a specific binding pocket for the D-Tyr of this substrate

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

Acyl-homoserine lactone acylase PvdQ

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

5ubk__assembly_1__model_1

5ubk__assembly_1__model_1 | I(q)

5ubk__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) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Inactive S1A/N269D-cpPvdQ mutant in complex with the pyoverdine precursor PVDIq reveals a specific binding pocket for the D-Tyr of this substrate

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

Acyl-homoserine lactone acylase PvdQ

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

5ubk__assembly_1__model_1

5ubk__assembly_1__model_1 | I(q)

5ubk__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) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)