3ly3

Crystal Structure of fluorophore-labeled Class A Beta-lactamase PenP

Method: X-RAY DIFFRACTION D_max: 59.7 Å Quality: REASONABLE

▼

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

Beta-lactamase

Bacillus licheniformis

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 47–305	Fragment：residues 47-303 Mutation：E166C	No other associated polymer	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

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 3LY3	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 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 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
3LY4 Crystal Structure of fluorophore-labeled Class A -lactamase PenP-E166Cb in complex with penicillin G 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 47–303（257 aa） 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
3M2J Crystal Structure of fluorescein-labeled Class A -lactamase PenP Deposited 2010-03-07	Different construct 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 construct 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 construct 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 construct 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 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 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 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 1–259； UniProt 47–305

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	3ly3
Deposition date deposition_date	2010-02-26
Structure title title	Crystal Structure of fluorophore-labeled Class A Beta-lactamase PenP
Keywords keywords	beta-lactamase, fluorophore, biosensor, hydrolase, Antibiotic resistance, Cell membrane, Lipoprotein, Membrane, Palmitate; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	18.96 Å
Radius of gyration Rg (electron density) rg_electron	17.74 Å
Forward intensity I(0) i0	14683000.00
Molecular weight molecular_weight	28780.0 kDa
Excluded volume excluded_volume	36043 Å³
Envelope volume envelope_volume	40517 Å³
Hydration-shell volume shell_volume	18882 Å³
Envelope diameter envelope_diameter	61.4 Å
Shell Rg shell_rg	24.29 Å
Envelope Rg envelope_rg	18.01 Å
Shape Rg shape_rg	17.73 Å
Total Rg total_rg	18.71 Å
Total atoms total_atoms	2025
Residues n_residues	259
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

▼

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

Maximum dimension Dmax dmax	59.7 Å
Rg (real space) rg_real	18.85 Å
Rg uncertainty (real space) rg_real_error	0.35 Å
I(0) (real space) i0_real	1.4680e+07
I(0) uncertainty (real space) i0_real_error	1.7380e+05
Rg (reciprocal space) rg_reciprocal	18.87 Å
I(0) (reciprocal space) i0_reciprocal	14680000.0000
Solution quality estimate total_estimate	0.6732
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.1 Å
Skewness Skewness skewness	0.182
Kurtosis Kurtosis kurtosis	-0.358
Angular range angular_range	— – 0.4200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3419000.0000
Real-space data points n_real_points	73
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.878; Stabil: 0.999; Sysdev: 0.374; Positv: 1.000; Valcen: 0.994; Smooth: 0.000

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

▼

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3ly3a_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.3 — beta-lactamase/transpeptidase-like
Superfamily Superfamily superfamily	e.3.1 — beta-lactamase/transpeptidase-like
Family Family family	e.3.1.1 — beta-Lactamase/D-ala carboxypeptidase

CATH v4.4 (1 domains)

Domain ID domain_id	3ly3A00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	710 — Beta-lactamase
Homologous superfamily homologous superfamily	10 — DD-peptidase/beta-lactamase superfamily

▶

8. Citations (1)

▶

Unit-cell length a length_a	43.438 Å
Unit-cell length b length_b	74.936 Å
Unit-cell length c length_c	79.034 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	1.800 Å
Low-resolution limit resolution_low	39.530 Å
R factor r_factor	0.2236
R_work r_work	0.2216
R_free r_free	0.2608

Description description	Beta-lactamase
Molecular weight formula_weight	28839.6 kDa
EC 编号 ec_number	3.5.2.6
Mutation mutation	E166C
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2229

Crystal Structure of fluorophore-labeled Class A Beta-lactamase PenP

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

Beta-lactamase

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Bacillus licheniformis
NCBI Class编号 ncbi_taxonomy_id	1402
宿主生物 host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	204

fit	/app/data/saxs_computation/ly/3ly3/3ly3.fit
pddf	/app/data/pr_computation/ly/3ly3/3ly3.pr.out
profile	/app/data/saxs_computation/ly/3ly3/3ly3.dat