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3ly4

Crystal Structure of fluorophore-labeled Class A -lactamase PenP-E166Cb in complex with penicillin G

Method: X-RAY DIFFRACTION Dmax: 60.7 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Beta-lactamase

Bacillus licheniformis

UniProt P00808

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 47–303 Fragment：residues 47-301 Mutation：E166C PNM OPEN FORM - PENICILLIN G × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 1.80 Å R-free 0.260

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 3LY4 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1I2S BETA-LACTAMASE FROM BACILLUS LICHENIFORMIS BS3 Deposited 2001-02-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 26–307（282 aa）
Chain B 26–307（282 aa）
Not recorded NA SODIUM ION × 2 CIT CITRIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；PEG 6000, sodium citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.70 Å R-free 0.237
1I2W BETA-LACTAMASE FROM BACILLUS LICHENIFORMIS BS3 COMPLEXED WITH CEFOXITIN Deposited 2001-02-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 26–307（282 aa）
Chain B 26–307（282 aa）
Not recorded 1QL (2R)-5-[(carbamoyloxy)methyl]-2-{(1S)-1-methoxy-2-oxo-1-[(thiophen-2-ylacetyl)amino]ethyl}-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid × 2 OUT CARBAMIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；PEG 6000, sodium citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.70 Å R-free 0.256
1MBL A catalytically-impaired class A beta-lactamase: 2 Angstroms crystal structure and kinetics of the Bacillus licheniformis E166A mutant Deposited 1992-08-17 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 48–303（256 aa）
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.00 Å
1MBL A catalytically-impaired class A beta-lactamase: 2 Angstroms crystal structure and kinetics of the Bacillus licheniformis E166A mutant Deposited 1992-08-17 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 48–303（256 aa）
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.00 Å
2BLM BETA-LACTAMASE OF BACILLUS LICHENIFORMIS 749(SLASH)C AT 2 ANGSTROMS RESOLUTION Deposited 1990-02-02 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 43–307（265 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.00 Å
2BLM BETA-LACTAMASE OF BACILLUS LICHENIFORMIS 749(SLASH)C AT 2 ANGSTROMS RESOLUTION Deposited 1990-02-02 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 43–307（265 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.00 Å
3LY3 Crystal Structure of fluorophore-labeled Class A Beta-lactamase PenP Deposited 2010-02-26 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 47–305（259 aa） Fragment：residues 47-303
Mutation：E166C No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.80 Å R-free 0.261
3M2J Crystal Structure of fluorescein-labeled Class A -lactamase PenP Deposited 2010-03-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 47–303（257 aa） Fragment：residues 47-301
Mutation：E166C SO4 SULFATE ION × 1 F5M 5-(2,5-dioxo-2,5-dihydro-1H-pyrrol-1-yl)-2-(6-hydroxy-3-oxo-3H-xanthen-9-yl)benzoic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；291 K；PEG 4000, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.80 Å R-free 0.273
3M2J Crystal Structure of fluorescein-labeled Class A -lactamase PenP Deposited 2010-03-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 47–303（257 aa） Fragment：residues 47-301
Mutation：E166C SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；291 K；PEG 4000, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.80 Å R-free 0.273
3M2K Crystal Structure of fluorescein-labeled Class A -beta lactamase PenP in complex with cefotaxime Deposited 2010-03-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 47–303（257 aa） Fragment：residues 47-301
Mutation：E166C CEF CEFOTAXIME, C3' cleaved, open, bound form × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；291 K；PEG 4000, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.50 Å R-free 0.236
3M2K Crystal Structure of fluorescein-labeled Class A -beta lactamase PenP in complex with cefotaxime Deposited 2010-03-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 47–303（257 aa） Fragment：residues 47-301
Mutation：E166C CEF CEFOTAXIME, C3' cleaved, open, bound form × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；291 K；PEG 4000, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.50 Å R-free 0.236
3SH7 Crystal structure of fluorophore-labeled beta-lactamase PenP Deposited 2011-06-16 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 43–307（265 aa） Fragment：Small exopenicillinase
Mutation：E166C BB0 1-[6-(dimethylamino)naphthalen-2-yl]ethanone × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；PEG4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.50 Å R-free 0.244
3SH7 Crystal structure of fluorophore-labeled beta-lactamase PenP Deposited 2011-06-16 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 43–307（265 aa） Fragment：Small exopenicillinase
Mutation：E166C BB0 1-[6-(dimethylamino)naphthalen-2-yl]ethanone × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；PEG4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.50 Å R-free 0.244
3SH8 Crystal structure of fluorophore-labeled beta-lactamase PenP in complex with cephaloridine Deposited 2011-06-16 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 43–307（265 aa） Fragment：Small exopenicillinase
Mutation：E166C CED 5-METHYL-2-[2-OXO-1-(2-THIOPHEN-2-YL-ACETYLAMINO)-ETHYL]-3,6-DIHYDRO-2H-[1,3]THIAZINE-4-CARBOXYLIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；PEG4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.00 Å R-free 0.267
3SH8 Crystal structure of fluorophore-labeled beta-lactamase PenP in complex with cephaloridine Deposited 2011-06-16 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 43–307（265 aa） Fragment：Small exopenicillinase
Mutation：E166C CED 5-METHYL-2-[2-OXO-1-(2-THIOPHEN-2-YL-ACETYLAMINO)-ETHYL]-3,6-DIHYDRO-2H-[1,3]THIAZINE-4-CARBOXYLIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；PEG4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.00 Å R-free 0.267
3SH9 Crystal structure of fluorophore-labeled beta-lactamase PenP in complex with cefotaxime Deposited 2011-06-16 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 43–307（265 aa） Fragment：Small exopenicillinase
Mutation：E166C CEF CEFOTAXIME, C3' cleaved, open, bound form × 1 BB0 1-[6-(dimethylamino)naphthalen-2-yl]ethanone × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；PEG4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.90 Å R-free 0.246
3SH9 Crystal structure of fluorophore-labeled beta-lactamase PenP in complex with cefotaxime Deposited 2011-06-16 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 43–307（265 aa） Fragment：Small exopenicillinase
Mutation：E166C CEF CEFOTAXIME, C3' cleaved, open, bound form × 1 BB0 1-[6-(dimethylamino)naphthalen-2-yl]ethanone × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；PEG4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.90 Å R-free 0.246
3SOI Crystallographic structure of Bacillus licheniformis beta-lactamase W210F/W229F/W251F at 1.73 angstrom resolution Deposited 2011-06-30 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 46–303（258 aa） Fragment：BETA-LACTAMASE (UNP Residues 46-303)
Mutation：W210F, W229F, W251F CIT CITRIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；293 K；PEG 4000 28%, Sodium Citrate 0.1 M, pH 5.4, vapor diffusion, hanging drop, temperature 293K
Resolution 1.73 Å R-free 0.193
3SOI Crystallographic structure of Bacillus licheniformis beta-lactamase W210F/W229F/W251F at 1.73 angstrom resolution Deposited 2011-06-30 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 46–303（258 aa） Fragment：BETA-LACTAMASE (UNP Residues 46-303)
Mutation：W210F, W229F, W251F CIT CITRIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；293 K；PEG 4000 28%, Sodium Citrate 0.1 M, pH 5.4, vapor diffusion, hanging drop, temperature 293K
Resolution 1.73 Å R-free 0.193
4BLM BETA-LACTAMASE OF BACILLUS LICHENIFORMIS 749(SLASH)C. REFINEMENT AT 2 ANGSTROMS RESOLUTION AND ANALYSIS OF HYDRATION Deposited 1991-05-28 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 43–307（265 aa）
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.00 Å
4BLM BETA-LACTAMASE OF BACILLUS LICHENIFORMIS 749(SLASH)C. REFINEMENT AT 2 ANGSTROMS RESOLUTION AND ANALYSIS OF HYDRATION Deposited 1991-05-28 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 43–307（265 aa）
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.00 Å
4M3K Structure of a single domain camelid antibody fragment cAb-H7S in complex with the BlaP beta-lactamase from Bacillus licheniformis Deposited 2013-08-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 44–307（264 aa） Fragment：UNP residues 44-307
Not recorded CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.2 uL 0.2 M (NH4)Cl 20 % PEG3350 + 0.2 uL complex 14.2 mg/ml 20 mM tris, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.48 Å R-free 0.195
4N1H Structure of a single-domain camelid antibody fragment cAb-F11N in complex with the BlaP beta-lactamase from Bacillus licheniformis Deposited 2013-10-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 44–307（264 aa） Fragment：UNP residues 44-307
Mutation：ProGly insertion between residues 197 and 198 No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；0.1 uL acetate 0.1 M, pH 4.6, 12 % P4K + 0.1 uL protein complex at 14 mg/mL in Tris 20 mM, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 3.00 Å R-free 0.284
4N1H Structure of a single-domain camelid antibody fragment cAb-F11N in complex with the BlaP beta-lactamase from Bacillus licheniformis Deposited 2013-10-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 44–307（264 aa） Fragment：UNP residues 44-307
Mutation：ProGly insertion between residues 197 and 198 No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；0.1 uL acetate 0.1 M, pH 4.6, 12 % P4K + 0.1 uL protein complex at 14 mg/mL in Tris 20 mM, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 3.00 Å R-free 0.284
4N92 Crystal structure of beta-lactamse PenP_E166S Deposited 2013-10-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 43–307（265 aa） Fragment：Small exopenicillinase
Chain B 43–307（265 aa） Fragment：Small exopenicillinase
Mutation：E166S Mutation：E166S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；289 K；Tris, PEG 3350, ammonium acetate, pH 8.0, vapor diffusion, hanging drop, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 1.93 Å R-free 0.230
4N9K crystal structure of beta-lactamse PenP_E166S in complex with cephaloridine Deposited 2013-10-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 43–307（265 aa） Fragment：Small exopenicillinase
Chain B 43–307（265 aa） Fragment：Small exopenicillinase
Mutation：E166S Mutation：E166S CED 5-METHYL-2-[2-OXO-1-(2-THIOPHEN-2-YL-ACETYLAMINO)-ETHYL]-3,6-DIHYDRO-2H-[1,3]THIAZINE-4-CARBOXYLIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；289 K；Tris, PEG 3350, ammonium acetate, pH 8.0, vapor diffusion, hanging drop, temperature 289K
Resolution 1.93 Å R-free 0.229
4N9L crystal structure of beta-lactamse PenP_E166S in complex with meropenem Deposited 2013-10-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 43–307（265 aa） Fragment：Small exopenicillinase
Chain B 43–307（265 aa） Fragment：Small exopenicillinase
Mutation：E166S Mutation：E166S DWZ (2S,3R,4S)-4-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-2-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-3-methyl-3,4-dihydro-2H-pyrrole-5-carboxylic acid × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；289 K；Tris, PEG 3350, ammonium acetate, pH 8.0, vapor diffusion, hanging drop, temperature 289K
Resolution 2.30 Å R-free 0.242
5GHX Crystal structure of beta-lactamase PenP mutant-E166H Deposited 2016-06-21 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 43–307（265 aa） Fragment：UNP residues 43-307
Mutation：E166H ACY ACETIC ACID × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；0.1M Tris pH 8.0, 22.5% PEG 3350, 0.4M ammonium acetate
Resolution 1.24 Å R-free 0.161
5GHX Crystal structure of beta-lactamase PenP mutant-E166H Deposited 2016-06-21 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 43–307（265 aa） Fragment：UNP residues 43-307
Mutation：E166H ACY ACETIC ACID × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；0.1M Tris pH 8.0, 22.5% PEG 3350, 0.4M ammonium acetate
Resolution 1.24 Å R-free 0.161
5GHY Crystal structure of beta-lactamase PenP mutant-E166H in complex with cephaloridine as "post-acylation" intermediate Deposited 2016-06-21 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 B 43–307（265 aa） Fragment：UNP residues 43-307
Mutation：E166H CED 5-METHYL-2-[2-OXO-1-(2-THIOPHEN-2-YL-ACETYLAMINO)-ETHYL]-3,6-DIHYDRO-2H-[1,3]THIAZINE-4-CARBOXYLIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；0.1M Tris pH 8.0, 22.5% PEG 3350, 0.4M ammonium acetate
Resolution 2.10 Å R-free 0.240
5GHY Crystal structure of beta-lactamase PenP mutant-E166H in complex with cephaloridine as "post-acylation" intermediate Deposited 2016-06-21 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 43–307（265 aa） Fragment：UNP residues 43-307
Mutation：E166H CED 5-METHYL-2-[2-OXO-1-(2-THIOPHEN-2-YL-ACETYLAMINO)-ETHYL]-3,6-DIHYDRO-2H-[1,3]THIAZINE-4-CARBOXYLIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；0.1M Tris pH 8.0, 22.5% PEG 3350, 0.4M ammonium acetate
Resolution 2.10 Å R-free 0.240
5GHZ Crystal structure of beta-lactamase PenP mutant-E166H in complex with cephaloridine as "pre-deacylation" intermediate Deposited 2016-06-21 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 B 43–307（265 aa） Fragment：UNP residues 43-307
Mutation：E166H CED 5-METHYL-2-[2-OXO-1-(2-THIOPHEN-2-YL-ACETYLAMINO)-ETHYL]-3,6-DIHYDRO-2H-[1,3]THIAZINE-4-CARBOXYLIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；0.1M Tris pH 8.0, 22.5% PEG 3350, 0.4M ammonium acetate
Resolution 1.93 Å R-free 0.204
5GHZ Crystal structure of beta-lactamase PenP mutant-E166H in complex with cephaloridine as "pre-deacylation" intermediate Deposited 2016-06-21 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 43–307（265 aa） Fragment：UNP residues 43-307
Mutation：E166H CED 5-METHYL-2-[2-OXO-1-(2-THIOPHEN-2-YL-ACETYLAMINO)-ETHYL]-3,6-DIHYDRO-2H-[1,3]THIAZINE-4-CARBOXYLIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；0.1M Tris pH 8.0, 22.5% PEG 3350, 0.4M ammonium acetate
Resolution 1.93 Å R-free 0.204
5LWF Structure of a single domain camelid antibody fragment cAb-G10S in complex with the BlaP beta-lactamase from Bacillus licheniformis Deposited 2016-09-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 44–307（264 aa）
Not recorded ACT ACETATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Mg Acetate, 0.1 M NaCacodylate pH 6.5, 20% PEG8000
Resolution 2.56 Å R-free 0.242
5LWF Structure of a single domain camelid antibody fragment cAb-G10S in complex with the BlaP beta-lactamase from Bacillus licheniformis Deposited 2016-09-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 44–307（264 aa）
Not recorded ACT ACETATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Mg Acetate, 0.1 M NaCacodylate pH 6.5, 20% PEG8000
Resolution 2.56 Å R-free 0.242
5ZFL Crystal structure of beta-lactamase PenP mutant E166Y Deposited 2018-03-06 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 43–307（265 aa）
Mutation：E166Y EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；0.1M Tris pH8.0, 25% PEG 3350, 0.2M ammonium acetate
Resolution 1.50 Å R-free 0.209
5ZFL Crystal structure of beta-lactamase PenP mutant E166Y Deposited 2018-03-06 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 43–307（265 aa）
Mutation：E166Y EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；0.1M Tris pH8.0, 25% PEG 3350, 0.2M ammonium acetate
Resolution 1.50 Å R-free 0.209
5ZFT Crystal structure of beta-lactamase PenP mutant-E166Y in complex with cephaloridine as "pre-deacylation" intermediate Deposited 2018-03-07 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 43–307（265 aa）
Mutation：E166Y CED 5-METHYL-2-[2-OXO-1-(2-THIOPHEN-2-YL-ACETYLAMINO)-ETHYL]-3,6-DIHYDRO-2H-[1,3]THIAZINE-4-CARBOXYLIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；0.1M Tris pH8.0, 25% PEG 33500, 4M ammonium acetate
Resolution 1.93 Å R-free 0.218
5ZFT Crystal structure of beta-lactamase PenP mutant-E166Y in complex with cephaloridine as "pre-deacylation" intermediate Deposited 2018-03-07 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 43–307（265 aa）
Mutation：E166Y CED 5-METHYL-2-[2-OXO-1-(2-THIOPHEN-2-YL-ACETYLAMINO)-ETHYL]-3,6-DIHYDRO-2H-[1,3]THIAZINE-4-CARBOXYLIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；0.1M Tris pH8.0, 25% PEG 33500, 4M ammonium acetate
Resolution 1.93 Å R-free 0.218
5ZG6 Crystal structure of beta-lactamase PenP mutant-E166Y in complex with cephaloridine as "post-acylation" intermediate Deposited 2018-03-07 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 B 43–307（265 aa）
Mutation：E166Y CED 5-METHYL-2-[2-OXO-1-(2-THIOPHEN-2-YL-ACETYLAMINO)-ETHYL]-3,6-DIHYDRO-2H-[1,3]THIAZINE-4-CARBOXYLIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；0.1M Tris pH8.0, 25% PEG 3350, 0.4M ammonium acetate
Resolution 2.00 Å R-free 0.258
5ZG6 Crystal structure of beta-lactamase PenP mutant-E166Y in complex with cephaloridine as "post-acylation" intermediate Deposited 2018-03-07 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 43–307（265 aa）
Mutation：E166Y CED 5-METHYL-2-[2-OXO-1-(2-THIOPHEN-2-YL-ACETYLAMINO)-ETHYL]-3,6-DIHYDRO-2H-[1,3]THIAZINE-4-CARBOXYLIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；0.1M Tris pH8.0, 25% PEG 3350, 0.4M ammonium acetate
Resolution 2.00 Å R-free 0.258
9T9P Adenosine receptor A2a (A2AR)-beta-lactamase fusion bound to beta-lactamase inhibitory protein II (BLIPII) and ZM241385 Deposited 2025-11-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 47–300（254 aa）
Not recorded ZMA 4-{2-[(7-amino-2-furan-2-yl[1,2,4]triazolo[1,5-a][1,3,5]triazin-5-yl)amino]ethyl}phenol × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å

25 other PDB entries and 42 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name BLAC_BACLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–257； UniProt 47–303

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 3ly4

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3ly4
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3ly4
Deposition date deposition_date2010-02-26
Structure title titleCrystal Structure of fluorophore-labeled Class A -lactamase PenP-E166Cb in complex with penicillin G
Keywords keywordsbeta-lactamase, fluorophore, biosensor, hydrolase, Antibiotic resistance, Cell membrane, Lipoprotein, Membrane, Palmitate; HYDROLASE
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_guinier18.74 Å
Radius of gyration Rg (electron density) rg_electron17.53 Å
Forward intensity I(0) i014667700.00
Molecular weight molecular_weight28812.0 kDa
Excluded volume excluded_volume36094 ų
Envelope volume envelope_volume40050 ų
Hydration-shell volume shell_volume18809 ų
Envelope diameter envelope_diameter60.6 Å
Shell Rg shell_rg24.11 Å
Envelope Rg envelope_rg17.87 Å
Shape Rg shape_rg17.53 Å
Total Rg total_rg18.48 Å
Total atoms total_atoms2028
Residues n_residues257
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 dmax60.7 Å
Rg (real space) rg_real18.63 Å
Rg uncertainty (real space) rg_real_error0.36 Å
I(0) (real space) i0_real1.4670e+07
I(0) uncertainty (real space) i0_real_error1.8500e+05
Rg (reciprocal space) rg_reciprocal18.65 Å
I(0) (reciprocal space) i0_reciprocal14670000.0000
Solution quality estimate total_estimate0.8084
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary24.1 Å
Skewness Skewness skewness0.192
Kurtosis Kurtosis kurtosis-0.339
Angular range angular_range— – 0.4250 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3642000.0000
Real-space data points n_real_points74
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.837; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd3ly4a_
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_id3ly4A00
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)