SAXSdb — 7thq

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

L-proline--[L-prolyl-carrier protein] ligase

Pseudomonas protegens Pf-5

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Probable acyl carrier protein PigG × 1 （Q5W265） AZIDE ION × 3 ;5'-deoxy-5'-({(2S)-2-({2-[(N-{(2R)-4-[(dioxo-lambda~5~-phosphanyl)oxy]-2-hydroxy-3,3-dimethylbutanoyl}-beta-alanyl)amino]ethyl}sulfanyl)-2-[(2S)-pyrrolidin-2-yl]ethanesulfonyl}amino)adenosine ; × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Probable acyl carrier protein PigG × 1 （Q5W265） AZIDE ION × 3 ;5'-deoxy-5'-({(2S)-2-({2-[(N-{(2R)-4-[(dioxo-lambda~5~-phosphanyl)oxy]-2-hydroxy-3,3-dimethylbutanoyl}-beta-alanyl)amino]ethyl}sulfanyl)-2-[(2S)-pyrrolidin-2-yl]ethanesulfonyl}amino)adenosine ; × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PLTF_PSEF5
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–498； UniProt 1–498 Author chain B； PDBConstruct 1–498； UniProt 1–498

Probable acyl carrier protein PigG

Serratia sp. ATCC 39006

UniProt Q5W265

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	L-proline--[L-prolyl-carrier protein] ligase × 1 （Q4KCY5） AZIDE ION × 3 ;5'-deoxy-5'-({(2S)-2-({2-[(N-{(2R)-4-[(dioxo-lambda~5~-phosphanyl)oxy]-2-hydroxy-3,3-dimethylbutanoyl}-beta-alanyl)amino]ethyl}sulfanyl)-2-[(2S)-pyrrolidin-2-yl]ethanesulfonyl}amino)adenosine ; × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	L-proline--[L-prolyl-carrier protein] ligase × 1 （Q4KCY5） AZIDE ION × 3 ;5'-deoxy-5'-({(2S)-2-({2-[(N-{(2R)-4-[(dioxo-lambda~5~-phosphanyl)oxy]-2-hydroxy-3,3-dimethylbutanoyl}-beta-alanyl)amino]ethyl}sulfanyl)-2-[(2S)-pyrrolidin-2-yl]ethanesulfonyl}amino)adenosine ; × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PIGG_SERS3
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–87； UniProt 1–87 Author chain E； PDBConstruct 1–87； UniProt 1–87

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	7thq
Deposition date deposition_date	2022-01-11
Structure title title	Crystal structure of PltF trapped with PigG using a proline adenosine vinylsulfonamide inhibitor
Keywords keywords	;nonribosomal peptide synthetase, NRPS, type II, biosynthesis, Ligase-Transport protein complex, LIGASE, LIGASE-LIGASE INHIBITOR complex ;; LIGASE/LIGASE 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.

7thq__assembly_1__model_1

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

Download this curve (.dat)

7thq__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7thq__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.89 Å
Rg (electron density)	23.58 Å
Total Rg	24.45 Å
Atom count	4328
Residues	584
Excluded volume	77104 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7thq__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`7thq__assembly_2__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 (5)

Entity 1 Entity 1 polymer

Description description	L-proline--[L-prolyl-carrier protein] ligase
Molecular weight formula_weight	56397.7 kDa
EC 编号 ec_number	6.2.1.53
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,A
Atom count atom_count	8613

MKLLHERMMHSLARYPRQTAVVDEQDALSYEALELRIREFVAMLCALGVGQGQRILLWAHKSVDLVAVMQAALRLGVVYVPVDPLSPVSRLEKIAGDSQAVLVLCTAARLEELAGSALAQVRSVVLDDPASAGYWRNIDTGSSVVPTLAIQPDDLAYILYTSGSTGVPKGVALSHGNALAFVDWACERYCFQPGERFANHAPLHFDLSVLDIYCALNVGATVCLVPESIAFSPRLLTDFIRQHEISIWYSVPSVLMMMMQDGDLLSDIQDTLRVLLFAGEPFPVKHLRDLRAAYADVRLANLFGPTETNVCTAFEVGAIDPERVLPVPIGTAASGNQVWAQKPDGSRCAVGEEGELVVQGPTVMLGYFAKPAQEGPYKTGDMVRQRPDGNYEYLGRRDDMLKVRGNRIERGEVEAALLAHPQVSEAAVLVVGEGMNAQLWGVLVAHTRDALSLIDLKRHCAQRLPRYMIIDKVLCLDALPRNANGKVDRFALARQVEGKLAAALEHHHHHHHH

Source Source

Source organism organism	Pseudomonas protegens Pf-5
NCBI taxonomy ID ncbi_taxonomy_id	220664
Host organism host_organism	Escherichia coli BL21

Entity 2 Entity 2 polymer

Description description	Probable acyl carrier protein PigG
Molecular weight formula_weight	10689.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,C

MLESKLINHIATQFLDGEKDGLDSQTPLFELNIVDSAAIFDLVDFLRQESKVSIGMQEIHPANFATVQSMVALVQRLKAHPEQGGAAWEHHHHHH

Source Source

Source organism organism	Serratia sp. ATCC 39006
NCBI taxonomy ID ncbi_taxonomy_id	104623
Host organism host_organism	Escherichia coli BL21

Entity 3 Entity 3 non-polymer

Description description	AZIDE ION
Molecular weight formula_weight	42.0 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	;5'-deoxy-5'-({(2S)-2-({2-[(N-{(2R)-4-[(dioxo-lambda~5~-phosphanyl)oxy]-2-hydroxy-3,3-dimethylbutanoyl}-beta-alanyl)amino]ethyl}sulfanyl)-2-[(2S)-pyrrolidin-2-yl]ethanesulfonyl}amino)adenosine ;
Molecular weight formula_weight	765.8 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	49

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	7thqA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	300 — GMP Synthetase; Chain A, domain 3
Homologous superfamily homologous superfamily	30 — ANL, C-terminal domain

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Unit-cell length a length_a	65.730 Å
Unit-cell length b length_b	132.680 Å
Unit-cell length c length_c	140.940 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	2.460 Å
Low-resolution limit resolution_low	96.610 Å
R factor r_factor	0.2086
R_work r_work	0.2061
R_free r_free	0.2550

Crystal structure of PltF trapped with PigG using a proline adenosine vinylsulfonamide inhibitor

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

L-proline--[L-prolyl-carrier protein] ligase

State in the Current Structure

Other States of the Same Protein in the Database

Probable acyl carrier protein PigG

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

7thq__assembly_1__model_1

7thq__assembly_1__model_1 | I(q)

7thq__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)

Crystal structure of PltF trapped with PigG using a proline adenosine vinylsulfonamide inhibitor

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

L-proline--[L-prolyl-carrier protein] ligase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Probable acyl carrier protein PigG

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

7thq__assembly_1__model_1

7thq__assembly_1__model_1 | I(q)

7thq__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)