← Back to search
2q9m

4-Substituted Trinems as Broad Spectrum-Lactamase Inhibitors: Structure-based Design, Synthesis and Biological Activity

Method: X-RAY DIFFRACTION Dmax: 69.6 Å Quality: GOOD
▼

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

Beta-lactamase

OrganismNot specified

UniProt P05364

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 22–380 Not recorded LK7 (1R,4S,7AS)-1-(1-FORMYLPROP-1-EN-1-YL)-4-METHOXY-2,4,5,6,7,7A-HEXAHYDRO-1H-ISOINDOLE-3-CARBOXYLIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；292 K；0.05M Cacodylate, 30% PEG8000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K Resolution 2.05 Å R-free 0.245

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 2Q9M Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1BLS CRYSTALLOGRAPHIC STRUCTURE OF A PHOSPHONATE DERIVATIVE OF THE ENTEROBACTER CLOACAE P99 CEPHALOSPORINASE: MECHANISTIC INTERPRETATION OF A BETA-LACTAMASE TRANSITION STATE ANALOG Deposited 1993-12-17 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 21–381（361 aa）
Not recorded IPP (P-IODOPHENYLACETYLAMINO)METHYLPHOSPHINIC ACID × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.30 Å
1BLS CRYSTALLOGRAPHIC STRUCTURE OF A PHOSPHONATE DERIVATIVE OF THE ENTEROBACTER CLOACAE P99 CEPHALOSPORINASE: MECHANISTIC INTERPRETATION OF A BETA-LACTAMASE TRANSITION STATE ANALOG Deposited 1993-12-17 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 21–381（361 aa）
Not recorded IPP (P-IODOPHENYLACETYLAMINO)METHYLPHOSPHINIC ACID × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.30 Å
1GCE STRUCTURE OF THE BETA-LACTAMASE OF ENTEROBACTER CLOACAE GC1 Deposited 1999-05-17 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 21–381（361 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5；298 K；VAPOR DIFFUSION, WITH 6.7 OR 8.0 MG/ML PROTEIN IN 5-7.5% PEG8000, 20-25MM POTASSIUM PHOSPHATE (MONOBASIC), OVER 12.5 OR 15% PEG8000, 50MM POTASSIUM PHOSPHATE (MONOBASIC) RESERVOIR AT ROOM TEMPERATURE., temperature 298K
Resolution 1.80 Å R-free 0.232
1RGZ Enterobacter cloacae GC1 Class C beta-Lactamase Complexed with Transition-State Analog of Cefotaxime Deposited 2003-11-13 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–384（363 aa）
Not recorded PTX {[(2E)-2-(2-AMINO-1,3-THIAZOL-4-YL)-2-(METHOXYIMINO)ETHANOYL]AMINO}METHYLPHOSPHONIC ACID × 1 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；296 K；PEG 8000, HEPES, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 296K
Resolution 1.37 Å R-free 0.195
1XX2 Refinement of P99 beta-lactamase from Enterobacter cloacae Deposited 2004-11-03 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 21–381（361 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；298 K；PEG 8000, SODIUM CACODYLATE, MgCl2, NaN3, pH 6.5 - 8.5, VAPOR DIFFUSION, temperature 298K
Resolution 1.88 Å R-free 0.214
1XX2 Refinement of P99 beta-lactamase from Enterobacter cloacae Deposited 2004-11-03 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 21–381（361 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；298 K；PEG 8000, SODIUM CACODYLATE, MgCl2, NaN3, pH 6.5 - 8.5, VAPOR DIFFUSION, temperature 298K
Resolution 1.88 Å R-free 0.214
1Y54 Crystal structure of the native class C beta-lactamase from Enterobacter cloacae 908R complexed with BRL42715 Deposited 2004-12-02 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 21–381（361 aa）
Not recorded FDT (7R)-6-FORMYL-7-(1-METHYL-1H-1,2,3-TRIAZOL-4-YL)-4,7-DIHYDRO-1,4-THIAZEPINE-3-CARBOXYLIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；298 K；PEG 6000 30%, bicine 100mM, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.10 Å R-free 0.292
2Q9N 4-Substituted Trinems as Broad Spectrum-Lactamase Inhibitors: Structure-based Design, Synthesis and Biological Activity Deposited 2007-06-13 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–380（359 aa）
Not recorded LK5 (1S,4R,7AR)-4-BUTOXY-1-[(1R)-1-FORMYLPROPYL]-2,4,5,6,7,7A-HEXAHYDRO-1H-ISOINDOLE-3-CARBOXYLIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.8；292 K；0.1M sodium acetate 0.2M ammonium acetate 22% PEG4000, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Resolution 2.20 Å R-free 0.315
3S4X Crystal structure of the Asn152Gly mutant of P99 beta-lactamase Deposited 2011-05-20 Different construct 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 21–381（361 aa）
Mutation：I16V, A88P, N152G, A299V SO4 SULFATE ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.15 M ammonium sulfate, 30% polyethylene glycol (PEG) 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.95 Å R-free 0.234
3S4X Crystal structure of the Asn152Gly mutant of P99 beta-lactamase Deposited 2011-05-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 21–381（361 aa）
Mutation：I16V, A88P, N152G, A299V SO4 SULFATE ION × 14 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.15 M ammonium sulfate, 30% polyethylene glycol (PEG) 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.95 Å R-free 0.234
4XUX Structure of ampC bound to RPX-7009 at 1.75 A Deposited 2015-01-26 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 21–381（361 aa） Fragment：UNP residues 21-381
Not recorded 4D6 Vaborbactam × 1 EDO 1,2-ETHANEDIOL × 2 PG0 2-(2-METHOXYETHOXY)ETHANOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；289 K；30mg/ml AmpC, 30% PEG3000, 0.1M TRIS, PH 7.0, 0.2M NACL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K
Resolution 1.75 Å R-free 0.186
5HAI P99 beta-lactamase mutant - S64G Deposited 2015-12-30 Different construct 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 21–381（361 aa） Fragment：UNP residues 21-381
Mutation：S64G PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；298 K；0.1M SPG buffer (succinic acid, sodium dihydrogen phosphate, and glycine) and 25% PEG 1500
Resolution 2.74 Å R-free 0.243
5XHR Crystal structure of P99 beta-lactamase in complex with a penicillin derivative MPC-1 Deposited 2017-04-24 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 21–381（361 aa） Fragment：UNP residues 21-381
Not recorded PXH (2~{R},4~{S})-5,5-dimethyl-2-[(2~{S},3~{R})-3-oxidanyl-1-oxidanylidene-5-thiophen-2-yl-pentan-2-yl]-1,3-thiazolidine-4-carboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；0.1M Bis-Tris pH 6.5, 25% PEG3350
Resolution 1.80 Å R-free 0.233
7TI1 Structure of AmpC bound to RPX-7063 at 2.0A Deposited 2022-01-12 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–381（381 aa）
Not recorded ZXQ {(3R,7S)-2-hydroxy-3-[2-(thiophen-2-yl)acetamido]-2,3,4,7-tetrahydro-1,2-oxaborepin-7-yl}acetic acid × 1 EDO 1,2-ETHANEDIOL × 2 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；30% PEG3000, 0.1M Tris pH 7.0, 0.2M NaCl
Resolution 2.00 Å R-free 0.214

11 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name AMPC_ENTCL
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–359； UniProt 22–380

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 2q9m

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2q9m
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id2q9m
Deposition date deposition_date2007-06-13
Structure title title4-Substituted Trinems as Broad Spectrum-Lactamase Inhibitors: Structure-based Design, Synthesis and Biological Activity
Keywords keywordsbeta-lactamase inhibitor, tricyclic carbapenem, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION
▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier20.72 Å
Radius of gyration Rg (electron density) rg_electron19.64 Å
Forward intensity I(0) i024726700.00
Molecular weight molecular_weight39255.0 kDa
Excluded volume excluded_volume49598 ų
Envelope volume envelope_volume56006 ų
Hydration-shell volume shell_volume23199 ų
Envelope diameter envelope_diameter73.2 Å
Shell Rg shell_rg26.82 Å
Envelope Rg envelope_rg19.96 Å
Shape Rg shape_rg19.63 Å
Total Rg total_rg20.62 Å
Total atoms total_atoms2770
Residues n_residues359
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
▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax69.6 Å
Rg (real space) rg_real20.60 Å
Rg uncertainty (real space) rg_real_error0.51 Å
I(0) (real space) i0_real2.4730e+07
I(0) uncertainty (real space) i0_real_error3.7480e+05
Rg (reciprocal space) rg_reciprocal20.63 Å
I(0) (reciprocal space) i0_reciprocal24730000.0000
Solution quality estimate total_estimate0.7905
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary27.2 Å
Skewness Skewness skewness0.217
Kurtosis Kurtosis kurtosis-0.310
Angular range angular_range— – 0.3850 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha9508000.0000
Real-space data points n_real_points70
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.763; Stabil: 0.995; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.000
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

▼

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd2q9ma_
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.3.1.1 — beta-Lactamase/D-ala carboxypeptidase

CATH v4.4 (1 domains)

Domain ID domain_id2q9mA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology710 — Beta-lactamase
Homologous superfamily homologous superfamily10 — DD-peptidase/beta-lactamase superfamily
▶

8. Citations (1)

▶

9. Files and Curves (10)