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6vbd

Crystal structure of transpeptidase domain of PBP2 from Neisseria gonorrhoeae cephalosporin-resistant strain H041 acylated by ceftriaxone

Method: X-RAY DIFFRACTION Dmax: 58.9 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Probable peptidoglycan D,D-transpeptidase PenA

Neisseria gonorrhoeae

UniProt F2Z7K9

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 237–575 Not recorded CEF CEFOTAXIME, C3' cleaved, open, bound form × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 9.3；291 K；40% PEG 600, 0.1M CHES Resolution 1.80 Å R-free 0.195

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 6VBD Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6VBC Crystal structure of transpeptidase domain of PBP2 from Neisseria gonorrhoeae cephalosporin-resistant strain H041 Deposited 2019-12-18 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 237–575（339 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.3；291 K；40% PEG 600, 0.1 M CHES
Resolution 1.55 Å R-free 0.200
8VBZ Crystal structure of the transpeptidase domain of a S310A mutant of PBP2 from Neisseria gonorrhoeae strain H041 Deposited 2023-12-13 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 237–575（339 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；32-40% PEG 600, 0.1 M CHES
Resolution 1.90 Å R-free 0.211
8VEN Crystal structure of transpeptidase domain of PBP2 from Neisseria gonorrhoeae cephalosporin-resistant strain H041 in complex with cefoperazone Deposited 2023-12-20 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 237–575（339 aa）
Not recorded A1ADP (2R,4R)-2-[(1R)-1-{[(2R)-2-[(4-ethyl-2,3-dioxopiperazine-1-carbonyl)amino]-2-(4-hydroxyphenyl)acetyl]amino}-2-oxoethyl]-5-methylidene-1,3-thiazinane-4-carboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；32-40% PEG 600, 0.1 M CHES
Resolution 1.80 Å R-free 0.201
8VEP Crystal structure of transpeptidase domain of PBP2 from Neisseria gonorrhoeae cephalosporin-resistant strain H041 acylated by piperacillin Deposited 2023-12-20 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 237–575（339 aa）
Not recorded JPP Piperacillin (Open Form) × 1 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.8；291 K；32-40% PEG 600, 0.1 M CHES
Resolution 2.00 Å R-free 0.206
8VEQ Crystal structure of transpeptidase domain of PBP2 from Neisseria gonorrhoeae cephalosporin-resistant strain H041 in complex with azlocillin Deposited 2023-12-20 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 237–575（339 aa）
Not recorded 59H (2R,4S)-5,5-dimethyl-2-[(1R)-2-oxo-1-{[(2R)-2-{[(2-oxoimidazolidin-1-yl)carbonyl]amino}-2-phenylacetyl]amino}ethyl]-1,3-thiazolidine-4-carboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.8；291 K；32-40% PEG 600, 0.1 M CHES
Resolution 2.40 Å R-free 0.250
9OSK Crystal structure of the transpeptidase domain of a Y422A mutant of PBP2 from Neisseria gonorrhoeae strain H041 Deposited 2025-05-24 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 237–575（339 aa）
Mutation：Y422A No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.60 Å R-free 0.253
9OSL Crystal structure of the transpeptidase domain of a Y422A mutant of PBP2 from Neisseria gonorrhoeae strain H041 acylated by ceftriaxone Deposited 2025-05-24 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 237–575（339 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.40 Å R-free 0.243
9Z5T Crystal structure of the transpeptidase domain of PBP2 from the Neisseria gonorrhoeae cephalosporin-resistant strain H041 in complex with boronate inhibitor VNRX-14079 Deposited 2025-11-12 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 237–575（339 aa）
Not recorded A1C02 (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 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.3；291 K；40% PEG 600, 0.1 M CHES
Resolution 2.10 Å R-free 0.236

8 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

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.

SAXS scattering curve SAXS Profile

SAXS profile for 6vbd

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6vbd
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6vbd
Deposition date deposition_date2019-12-18
Structure title titleCrystal structure of transpeptidase domain of PBP2 from Neisseria gonorrhoeae cephalosporin-resistant strain H041 acylated by ceftriaxone
Keywords keywordsPENICILLIN-BINDING PROTEIN, ACYLATION, ANTIBIOTIC RESISTANCE, HYDROLASE, HYDROLASE-ANTIBIOTIC complex; HYDROLASE/ANTIBIOTIC
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier19.47 Å
Radius of gyration Rg (electron density) rg_electron18.41 Å
Forward intensity I(0) i020699000.00
Molecular weight molecular_weight35329.0 kDa
Excluded volume excluded_volume44547 ų
Envelope volume envelope_volume49527 ų
Hydration-shell volume shell_volume21693 ų
Envelope diameter envelope_diameter58.9 Å
Shell Rg shell_rg25.53 Å
Envelope Rg envelope_rg18.73 Å
Shape Rg shape_rg18.41 Å
Total Rg total_rg19.35 Å
Total atoms total_atoms2485
Residues n_residues324
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax58.9 Å
Rg (real space) rg_real19.30 Å
Rg uncertainty (real space) rg_real_error0.20 Å
I(0) (real space) i0_real2.0700e+07
I(0) uncertainty (real space) i0_real_error2.2440e+05
Rg (reciprocal space) rg_reciprocal19.33 Å
I(0) (reciprocal space) i0_reciprocal20700000.0000
Solution quality estimate total_estimate0.7188
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary25.7 Å
Skewness Skewness skewness0.074
Kurtosis Kurtosis kurtosis-0.446
Angular range angular_range— – 0.4100 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha6572000.0000
Real-space data points n_real_points72
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.908; Stabil: 1.000; Sysdev: 0.226; Positv: 1.000; Valcen: 0.979; Smooth: 0.958
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd6vbda1
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.3 — beta-lactamase/transpeptidase-like
Superfamily Superfamily superfamilye.3.1 — beta-lactamase/transpeptidase-like
Family Family familye.3.1.0 — automated matches
Domain ID domain_idd6vbda2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id6vbdA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology710 — Beta-lactamase
Homologous superfamily homologous superfamily10 — DD-peptidase/beta-lactamase superfamily
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8. Citations (1)

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9. Files and Curves (10)