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4zam

Crystal structure of SHV-1 beta-lactamase bound to avibactam

Method: X-RAY DIFFRACTION Dmax: 62.0 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Beta-lactamase SHV-1

Klebsiella pneumoniae

UniProt P0AD64

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 22–286 Fragment：UNP residues 22-286 MA4 CYCLOHEXYL-HEXYL-BETA-D-MALTOSIDE × 2 NXL (2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；25% PEG6000, 100 mM Tris, pH 7.5, 0.56 mM Cymal-6 Resolution 1.42 Å R-free 0.193

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 4ZAM Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2G2U Crystal Structure of the SHV-1 Beta-lactamase/Beta-lactamase inhibitor protein (BLIP) complex Deposited 2006-02-16 Different construct 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 22–286（265 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 6.5；293 K；30% Ammonium SO4,25mM cacodylate, 10mM BisTris, 25mM NaCl , pH 6.5, EVAPORATION, temperature 293K
Resolution 1.60 Å R-free 0.186
2G2W Crystal Structure of the SHV D104K Beta-lactamase/Beta-lactamase inhibitor protein (BLIP) complex Deposited 2006-02-16 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 22–286（265 aa）
Mutation：D104K No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 6.5；293 K；4% PEG 8000, 25mM cacodylate, 10 mM BisTris, 25mM NaCl, pH 6.5, EVAPORATION, temperature 293K
Resolution 1.80 Å R-free 0.222
2H0Y Crystal structure of the M69V E166A double mutant of SHV-1 b-lactamase complexed to sulbactam Deposited 2006-05-15 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 22–286（265 aa）
Mutation：M69V, E166A TSL TRANS-ENAMINE INTERMEDIATE OF SULBACTAM × 1 MA4 CYCLOHEXYL-HEXYL-BETA-D-MALTOSIDE × 2 ESA ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；20% PEG 6000, 0.1 M HEPES, 0.56mM Cymal-6. Crystal soaked for 10 minutes in 50mM sublactam prior to freezing and data collection, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 1.70 Å R-free 0.211
2H10 Crystal structure of the M69V E166A double mutant of SHV-1 b-lactamase complexed to tazobactam Deposited 2006-05-15 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 22–286（265 aa）
Mutation：M69V, E166A TBE TAZOBACTAM INTERMEDIATE × 1 MA4 CYCLOHEXYL-HEXYL-BETA-D-MALTOSIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；20% PEG 6000, 0.1M HEPES, 0.56mM Cymal-6. Crystal soaked for 10 minutes in 50mM tazobactam prior to freezing and data collection, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 1.75 Å R-free 0.190
2ZD8 SHV-1 class A beta-lactamase complexed with meropenem Deposited 2007-11-20 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–286（265 aa）
Not recorded MA4 CYCLOHEXYL-HEXYL-BETA-D-MALTOSIDE × 2 MER (4R,5S)-3-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-5-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-4-methyl-4,5-d ihydro-1H-pyrrole-2-carboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；296 K；25% PEG6000, 0.1M HEPES, CYMAL-6, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 296K
Resolution 1.05 Å R-free 0.168
3C4O Crystal Structure of the SHV-1 Beta-lactamase/Beta-lactamase inhibitor protein (BLIP) E73M/S130K/S146M complex Deposited 2008-01-30 Different construct 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 22–286（265 aa）
Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.4；292 K；37.5% Ammonium Sulfate, 100mM Tris HCl, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Resolution 1.70 Å R-free 0.196
3C4P Crystal Structure of the SHV-1 Beta-lactamase/Beta-lactamase inhibitor protein (BLIP) E73M complex Deposited 2008-01-30 Different construct 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 22–286（265 aa）
Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.4；292 K；37.5% Ammonium Sulfate, 100mM Tris HCl, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Resolution 1.75 Å R-free 0.207
3D4F SHV-1 beta-lactamase complex with LN1-255 Deposited 2008-05-14 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–286（286 aa）
Not recorded MA4 CYCLOHEXYL-HEXYL-BETA-D-MALTOSIDE × 2 LN1 (3R)-4-{[(3,4-dihydroxyphenyl)acetyl]oxy}-N-(2-formylindolizin-3-yl)-3-sulfino-D-valine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；30% PEG6000, 0.1M HEPES pH7. 0.56mM Cymal-6, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 1.55 Å R-free 0.197
3MKE SHV-1 beta-lactamase complex with LP06 Deposited 2010-04-14 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–286（265 aa）
Not recorded MA4 CYCLOHEXYL-HEXYL-BETA-D-MALTOSIDE × 2 CB4 PINACOL[[2-AMINO-ALPHA-(1-CARBOXY-1-METHYLETHOXYIMINO)-4-THIAZOLEACETYL]AMINO]METHANEBORONATE × 1 CZ6 2-[(~{Z})-[1-(2-azanyl-1,3-thiazol-4-yl)-2-oxidanylidene-2-[[(6~{S})-4,4,6-trimethyl-1,3,2-dioxaborinan-2-yl]methylamino]ethylidene]amino]oxy-2-methyl-propanoic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；20-30% PEG 6000, 0.1M HEPES, 0.56Mm Cymal-6, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K
Resolution 1.75 Å R-free 0.181
3MKF SHV-1 beta-lactamase complex with GB0301 Deposited 2010-04-14 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–286（265 aa）
Not recorded CZ7 ({[(2R)-2-{[(4-ethyl-2,3-dioxo-3,4-dihydropyrazin-1(2H)-yl)carbonyl]amino}-2-(4-hydroxyphenyl)acetyl]amino}methyl)boronic acid × 1 MA4 CYCLOHEXYL-HEXYL-BETA-D-MALTOSIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；20-30% PEG 6000, 0.1M HEPES, 0.56Mm Cymal-6, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K
Resolution 1.33 Å R-free 0.190
3MXR SHV-1 beta-lactamase complex with compound 1 Deposited 2010-05-07 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–286（265 aa）
Not recorded CZ8 ({[(2R)-2-{[(4-ethyl-2,3-dioxopiperazin-1-yl)carbonyl]amino}-4-(4-hydroxyphenyl)butanoyl]amino}methyl)boronic acid × 1 MA4 CYCLOHEXYL-HEXYL-BETA-D-MALTOSIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；20-30% PEG 6000, 0.1M HEPES, 0.56Mm Cymal-6, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K
Resolution 1.30 Å R-free 0.203
3MXS SHV-1 beta-lactamase complex with compound 2 Deposited 2010-05-07 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–286（265 aa）
Not recorded CZ9 N-[(dihydroxyboranyl)methyl]-Nalpha-[(4-ethyl-2,3-dioxopiperazin-1-yl)carbonyl]-D-tyrosinamide × 1 MA4 CYCLOHEXYL-HEXYL-BETA-D-MALTOSIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；20-30% PEG 6000, 0.1M HEPES, 0.56Mm Cymal-6, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K
Resolution 1.24 Å R-free 0.194
3N4I Crystal structure of the SHV-1 D104E beta-lactamase/beta-lactamase inhibitor protein (BLIP) complex Deposited 2010-05-21 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 22–286（265 aa）
Mutation：D104E No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；40% ammonium sulfate, 100mM Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.56 Å R-free 0.179
3OPH ESBL R164S mutant of SHV-1 beta-lactamase Deposited 2010-09-01 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 1–286（286 aa）
Mutation：R164S MA4 CYCLOHEXYL-HEXYL-BETA-D-MALTOSIDE × 2 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；21-30% PEG 6000, 0.5mM cymal-6, 100mM HEPES buffer, pH 6.6-7.6, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 1.34 Å R-free 0.190
3OPL ESBL R164H mutant SHV-1 beta-lactamase Deposited 2010-09-01 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 1–286（286 aa）
Mutation：R164H MA4 CYCLOHEXYL-HEXYL-BETA-D-MALTOSIDE × 2 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；21-30% PEG 6000, 0.5mM cymal-6, 100mM HEPES buffer, pH 6.6-7.6, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 1.80 Å R-free 0.228
3OPP ESBL R164S mutant of SHV-1 beta-lactamase complexed with SA2-13 Deposited 2010-09-01 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 1–286（286 aa）
Mutation：R164S SA2 (3R)-4-[(4-CARBOXYBUTANOYL)OXY]-N-[(1E)-3-OXOPROP-1-EN-1-YL]-3-SULFINO-D-VALINE × 1 MA4 CYCLOHEXYL-HEXYL-BETA-D-MALTOSIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；21-30% PEG 6000, 0.5mM cymal-6, 100mM HEPES buffer, pH 6.6-7.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.80 Å R-free 0.192
3OPR ESBL R164H mutant of SHV-1 beta-lactamase complexed to SA2-13 Deposited 2010-09-01 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 1–286（286 aa）
Mutation：R164H MA4 CYCLOHEXYL-HEXYL-BETA-D-MALTOSIDE × 2 SA2 (3R)-4-[(4-CARBOXYBUTANOYL)OXY]-N-[(1E)-3-OXOPROP-1-EN-1-YL]-3-SULFINO-D-VALINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；21-30% PEG6000, 0.5mM cymal-6, 100mM HEPES buffer, pH 6.6-7.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.65 Å R-free 0.211
4FCF K234R: apo structure of inhibitor resistant beta-lactamase Deposited 2012-05-24 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 22–286（265 aa） Fragment：unp residues 22-286
Mutation：K234R MA4 CYCLOHEXYL-HEXYL-BETA-D-MALTOSIDE × 2 TAU 2-AMINOETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；296 K；21-30% PEG6K, 0.1M Hepes pH 6.6-7.6, 0.56mM cymal-6, VAPOR DIFFUSION, SITTING DROP, temperature 296K
Resolution 1.09 Å R-free 0.150
4FD8 Structure of apo S70C SHV beta-lactamase Deposited 2012-05-26 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 22–286（265 aa） Fragment：unp residues 22-286
Mutation：S70C MA4 CYCLOHEXYL-HEXYL-BETA-D-MALTOSIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；296 K；21-30% PEG6k, 0.1M hepes pH 6.8-7.8, 0.56mM cymal-6, VAPOR DIFFUSION, SITTING DROP, temperature 296K
Resolution 1.52 Å R-free 0.197
4FH2 Structure of s70c beta-lactamase bound to sulbactam Deposited 2012-06-05 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 22–286（265 aa） Fragment：unp residues 22-286
Mutation：S70C MA4 CYCLOHEXYL-HEXYL-BETA-D-MALTOSIDE × 2 0RN SULBACTAM × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；296 K；21-30%PEG6k, 0.1M hepes, 0.56mM cymal-6, VAPOR DIFFUSION, SITTING DROP, temperature 296K
Resolution 1.44 Å R-free 0.220
4FH4 high-resolution structure of apo wt SHV-1 beta-lactamase Deposited 2012-06-05 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–286（265 aa） Fragment：unp residues 22-286
Not recorded MA4 CYCLOHEXYL-HEXYL-BETA-D-MALTOSIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；296 K；21-30% peg6k, 0.1M hepes, 0.56mM cymal-6, pH 6.8-7.8, VAPOR DIFFUSION, SITTING DROP, temperature 296K
Resolution 1.09 Å R-free 0.166
4GD6 SHV-1 beta-lactamase in complex with penam sulfone SA1-204 Deposited 2012-07-31 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–286（286 aa）
Not recorded 17K (3R)-N-(2-formylindolizin-3-yl)-4-[(phenylacetyl)oxy]-3-sulfino-D-valine × 1 MA4 CYCLOHEXYL-HEXYL-BETA-D-MALTOSIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；25% PEG 6000, 100mM HEPES pH 7.0, 0.56mM Cymal-6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.53 Å R-free 0.194
4GD8 SHV-1 beta-lactamase in complex with penam sulfone SA3-53 Deposited 2012-07-31 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–286（286 aa）
Not recorded MXF (2S,3R)-4-(2-aminoethylcarbamoyloxy)-2-[(2-methanoylindolizin-3-yl)amino]-3-methyl-3-sulfino-butanoic acid × 1 MA4 CYCLOHEXYL-HEXYL-BETA-D-MALTOSIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；25% PEG 6000, 100mM HEPES pH7.0, 0.56mM Cymal-6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.60 Å R-free 0.242
4GDB SHV-1 in complex with 4H-pyrazolo[1,5-c][1,3]thiazole containing penem inhibitor Deposited 2012-07-31 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–286（286 aa）
Not recorded 17O (7R)-6-formyl-7-(4H-pyrazolo[1,5-c][1,3]thiazol-2-yl)-4,7-dihydro-1,4-thiazepine-3-carboxylic acid × 1 MA4 CYCLOHEXYL-HEXYL-BETA-D-MALTOSIDE × 2 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；25% PEG 6000, 100mM HEPES pH7.0, 0.56mM Cymal-6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.84 Å R-free 0.234
4JPM Structure of SHV-1 beta-lactamase in complex with the 7-alkylidenecephalosporin DCM-1-10 at 1.14 Ang resolution Deposited 2013-03-19 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–286（286 aa） Fragment：SVH-1 beta-lactamase
Not recorded MA4 CYCLOHEXYL-HEXYL-BETA-D-MALTOSIDE × 2 1OG 7-alkylidenecephalosporin DCM-1-10, bound form × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；21-30% PEG 6000, 0.1M HEPES buffer, 0.56mM Cymal-6, pH 6.8-7.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.14 Å R-free 0.164
4MBF Crystal structure of Penam sulfone PSR-4-157 bound to SHV-1 beta-lactamase Deposited 2013-08-19 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–286（265 aa） Fragment：unp residues 22-286
Not recorded MA4 CYCLOHEXYL-HEXYL-BETA-D-MALTOSIDE × 2 2AW 6-({(2R,3S)-3-carboxy-2-methyl-3-[(3-oxopropyl)amino]-2-sulfinopropyl}oxy)-6-oxohexanoic acid × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；21-30% PEG 6000, 0.1M HEPES buffer, 0.56mM Cymal-6, pH 6.8-7.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.54 Å R-free 0.196
4MBH Penam sulfone PSR-3-226 bound to E166A variant of SHV-1 beta-lactamase Deposited 2013-08-19 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 22–286（265 aa） Fragment：SHV-1 beta-lactamase
Mutation：E166A MA4 CYCLOHEXYL-HEXYL-BETA-D-MALTOSIDE × 2 0RJ 3-(formylamino)-L-alanine × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；21-30% PEG 6000, 0.1M HEPES. 0.56mM Cymal-6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.22 Å R-free 0.161
4MBK Crystal structure of K234R inhibitor-resistant variant of SHV beta-lactamase in complex with SA2-13 Deposited 2013-08-19 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 22–286（265 aa） Fragment：SHV-1 beta-lactamase
Mutation：K234R MA4 CYCLOHEXYL-HEXYL-BETA-D-MALTOSIDE × 2 SA2 (3R)-4-[(4-CARBOXYBUTANOYL)OXY]-N-[(1E)-3-OXOPROP-1-EN-1-YL]-3-SULFINO-D-VALINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；21-30% PEG 6000, 0.1M HEPES, 0.56mM Cymal-6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.46 Å R-free 0.214
4R3B Crystal structure of SHV-1 b-lactamase in complex with 6b-(hydroxymethyl)penicillanic acid sulfone PSR-283A Deposited 2014-08-14 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–286（265 aa） Fragment：SHV-1 beta-lactamase
Not recorded MA4 CYCLOHEXYL-HEXYL-BETA-D-MALTOSIDE × 2 3GE N-[(1E)-2-formyl-3-hydroxyprop-1-en-1-yl]-3-[(S)-sulfino]-D-valine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；21-30% PEG6000, 0.1M HEPES pH 6.2-8.2, 0.56mM Cymal-6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.37 Å R-free 0.172
5EE8 Crystal structure of S02030 boronic acid inhibitor complexed to SHV-1 beta-lactamase Deposited 2015-10-22 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–286（265 aa）
Not recorded ZXM 1-{(2R)-2-(dihydroxyboranyl)-2-[(thiophen-2-ylacetyl)amino]ethyl}-1H-1,2,3-triazole-4-carboxylic acid × 1 MA4 CYCLOHEXYL-HEXYL-BETA-D-MALTOSIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；20-30% PEG 6000, 100mM Tris pH 7.5, 0.56mM cymal-6
Resolution 1.54 Å R-free 0.175

30 other PDB entries and 30 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name BLA1_KLEPN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–265； UniProt 22–286

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 4zam

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4zam
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4zam
Deposition date deposition_date2015-04-13
Structure title titleCrystal structure of SHV-1 beta-lactamase bound to avibactam
Keywords keywordsHYDROLASE-HYDROLASE INHIBITOR complex; HYDROLASE/HYDROLASE INHIBITOR
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_guinier19.03 Å
Radius of gyration Rg (electron density) rg_electron17.77 Å
Forward intensity I(0) i016113700.00
Molecular weight molecular_weight29746.0 kDa
Excluded volume excluded_volume37052 ų
Envelope volume envelope_volume40879 ų
Hydration-shell volume shell_volume19009 ų
Envelope diameter envelope_diameter61.5 Å
Shell Rg shell_rg24.36 Å
Envelope Rg envelope_rg18.08 Å
Shape Rg shape_rg17.80 Å
Total Rg total_rg18.58 Å
Total atoms total_atoms2083
Residues n_residues265
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 dmax62.0 Å
Rg (real space) rg_real18.92 Å
Rg uncertainty (real space) rg_real_error0.34 Å
I(0) (real space) i0_real1.6110e+07
I(0) uncertainty (real space) i0_real_error1.9410e+05
Rg (reciprocal space) rg_reciprocal18.94 Å
I(0) (reciprocal space) i0_reciprocal16110000.0000
Solution quality estimate total_estimate0.8810
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-0.338
Angular range angular_range— – 0.4200 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2945000.0000
Real-space data points n_real_points73
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.833; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.953
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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) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd4zama_
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_id4zamA00
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)