SAXSdb — 9z5t

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

Probable peptidoglycan D,D-transpeptidase PenA

Neisseria gonorrhoeae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	;(3R)-7-fluoro-3-{[(2R)-2-(3-fluoro-4-phosphonophenyl)-2-{[3-(methanesulfonyl)-2-oxoimidazolidine-1-carbonyl]amino}acetyl]amino}-2-hydroxy-3,4-dihydro-2H-1,2-benzoxaborinine-8-carboxylic acid ; × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	F2Z7K9_NEIGO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–330； UniProt 237–575

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	9z5t
Deposition date deposition_date	2025-11-12
Structure title title	Crystal structure of the transpeptidase domain of PBP2 from the Neisseria gonorrhoeae cephalosporin-resistant strain H041 in complex with boronate inhibitor VNRX-14079
Keywords keywords	Neisseria gonorrhoeae, cephalosporin resistance, Penicillin-binding protein 2, Boronate inhibitor, ligase; LIGASE
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.

9z5t__assembly_1__model_1

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

Download this curve (.dat)

9z5t__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9z5t__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.50 Å
Rg (electron density)	18.42 Å
Total Rg	19.39 Å
Atom count	2473
Residues	321
Excluded volume	44162 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9z5t__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	Probable peptidoglycan D,D-transpeptidase PenA
Molecular weight formula_weight	35361.5 kDa
EC 编号 ec_number	3.4.16.4
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	2562

GSGGALSLDQRIQTLAYEELNKAVEYHQAKAGTVVVLDARTGEILALVNTPGRNRAVTDMIEPGSVMKPFPIAKALDSGKVDTTDTFNTLPYKIGPATVQDTHVYPTLDVRGIMQKSSNVGTSKLSAMFTPKEMYDFYHDLGVGVRMHSGFPGESAGVLRNWRKWRPIEQATMSFGYGLQLSLLQLARAYTVLTHDGELLPVSFEKQAVAPKGKRVIKASTAKKVRELMVSVTEAGGSGIAGAVDGFDVGAKTGTARKLVNGRYVDYKHVATFIGFAPAKNPRVIVAVTIDEPTANGYYSGVVTGPVFKQVMGGSLNILGVSPTKPLTNV

Source Source

Source organism organism	Neisseria gonorrhoeae
NCBI taxonomy ID ncbi_taxonomy_id	485
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	;(3R)-7-fluoro-3-{[(2R)-2-(3-fluoro-4-phosphonophenyl)-2-{[3-(methanesulfonyl)-2-oxoimidazolidine-1-carbonyl]amino}acetyl]amino}-2-hydroxy-3,4-dihydro-2H-1,2-benzoxaborinine-8-carboxylic acid ;
Molecular weight formula_weight	646.3 kDa
Source method src_method	nat
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	77

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Unit-cell length a length_a	49.865 Å
Unit-cell length b length_b	60.151 Å
Unit-cell length c length_c	111.023 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	4

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	40.830 Å
R factor r_factor	0.1930
R_work r_work	0.1910
R_free r_free	0.2360

Crystal structure of the transpeptidase domain of PBP2 from the Neisseria gonorrhoeae cephalosporin-resistant strain H041 in complex with boronate inhibitor VNRX-14079

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

Probable peptidoglycan D,D-transpeptidase PenA

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

9z5t__assembly_1__model_1

9z5t__assembly_1__model_1 | I(q)

9z5t__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

7. Citations (1)

Crystal structure of the transpeptidase domain of PBP2 from the Neisseria gonorrhoeae cephalosporin-resistant strain H041 in complex with boronate inhibitor VNRX-14079

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

Probable peptidoglycan D,D-transpeptidase PenA

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

9z5t__assembly_1__model_1

9z5t__assembly_1__model_1 | I(q)

9z5t__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

7. Citations (1)