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6jn5

Serine Beta-Lactamase KPC-2 in Complex with Dual MBL/SBL Inhibitor MS23

Method: X-RAY DIFFRACTION Dmax: 103.9 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Serine Beta-Lactamase KPC-2

Klebsiella pneumoniae

UniProt Q93LQ9

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 26–289 Not recorded BXU [(S)-(4-fluorophenyl)-[[(2S)-2-methyl-3-sulfanyl-propanoyl]amino]methyl]boronic acid × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；0.1M Lithium Sulphate, 0.05M Sodium Acetate (pH 4.5), 32-35% (v/v) Polyethylene glycol 8000 Resolution 1.97 Å R-free 0.316
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 26–289 Not recorded BXU [(S)-(4-fluorophenyl)-[[(2S)-2-methyl-3-sulfanyl-propanoyl]amino]methyl]boronic acid × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；0.1M Lithium Sulphate, 0.05M Sodium Acetate (pH 4.5), 32-35% (v/v) Polyethylene glycol 8000 Resolution 1.97 Å R-free 0.316
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain C； UniProt 26–289 Not recorded BXU [(S)-(4-fluorophenyl)-[[(2S)-2-methyl-3-sulfanyl-propanoyl]amino]methyl]boronic acid × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；0.1M Lithium Sulphate, 0.05M Sodium Acetate (pH 4.5), 32-35% (v/v) Polyethylene glycol 8000 Resolution 1.97 Å R-free 0.316
4 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain D； UniProt 26–289 Not recorded BXU [(S)-(4-fluorophenyl)-[[(2S)-2-methyl-3-sulfanyl-propanoyl]amino]methyl]boronic acid × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；0.1M Lithium Sulphate, 0.05M Sodium Acetate (pH 4.5), 32-35% (v/v) Polyethylene glycol 8000 Resolution 1.97 Å R-free 0.316

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 6JN5 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2OV5 Crystal structure of the KPC-2 carbapenemase Deposited 2007-02-13 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 30–290（261 aa）
Not recorded BCN BICINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9；293 K；16% PEG6000, 0.1M bicine, pH 9, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.85 Å R-free 0.190
2OV5 Crystal structure of the KPC-2 carbapenemase Deposited 2007-02-13 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 30–290（261 aa）
Not recorded BCN BICINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9；293 K；16% PEG6000, 0.1M bicine, pH 9, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.85 Å R-free 0.190
2OV5 Crystal structure of the KPC-2 carbapenemase Deposited 2007-02-13 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 30–290（261 aa）
Not recorded BCN BICINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9；293 K；16% PEG6000, 0.1M bicine, pH 9, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.85 Å R-free 0.190
3E2K Crystal Structure of the KPC-2 Beta-lactamase/Beta-lactamase inhibitor protein (BLIP) Deposited 2008-08-05 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 30–293（264 aa） Fragment：UNP residues 30-293
Mutation：G175S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；290 K；20% PEG 8000, 4% ethylene glycol, 100mM citrate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Resolution 2.10 Å R-free 0.234
3E2K Crystal Structure of the KPC-2 Beta-lactamase/Beta-lactamase inhibitor protein (BLIP) Deposited 2008-08-05 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 30–293（264 aa） Fragment：UNP residues 30-293
Mutation：G175S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；290 K；20% PEG 8000, 4% ethylene glycol, 100mM citrate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Resolution 2.10 Å R-free 0.234
3E2L Crystal Structure of the KPC-2 Beta-lactamase/Beta-lactamase inhibitor protein (BLIP) Deposited 2008-08-05 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 30–293（264 aa） Fragment：UNP residues 30-293
Mutation：G175S Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；290 K；20% PEG 8000, 6% ethylene glycol, 100mM citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Resolution 1.87 Å R-free 0.213
3E2L Crystal Structure of the KPC-2 Beta-lactamase/Beta-lactamase inhibitor protein (BLIP) Deposited 2008-08-05 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 30–293（264 aa） Fragment：UNP residues 30-293
Mutation：G175S Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；290 K；20% PEG 8000, 6% ethylene glycol, 100mM citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Resolution 1.87 Å R-free 0.213
6J8Q Serine Beta-Lactamase KPC-2 in Complex with Dual MBL/SBL Inhibitor WL-001 Deposited 2019-01-21 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 26–289（264 aa）
Not recorded BHU [[(2S)-2-methyl-3-sulfanyl-propanoyl]amino]methylboronic acid × 1 PEG DI(HYDROXYETHYL)ETHER × 7 ACY ACETIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；32% to 35% PEG 8000, 0.1M lithium sulphate, 0.05M sodium acetate (pH 4.5)
Resolution 1.79 Å R-free 0.205
6J8Q Serine Beta-Lactamase KPC-2 in Complex with Dual MBL/SBL Inhibitor WL-001 Deposited 2019-01-21 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 26–289（264 aa）
Not recorded BHU [[(2S)-2-methyl-3-sulfanyl-propanoyl]amino]methylboronic acid × 1 PEG DI(HYDROXYETHYL)ETHER × 4 ACY ACETIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；32% to 35% PEG 8000, 0.1M lithium sulphate, 0.05M sodium acetate (pH 4.5)
Resolution 1.79 Å R-free 0.205
6J8Q Serine Beta-Lactamase KPC-2 in Complex with Dual MBL/SBL Inhibitor WL-001 Deposited 2019-01-21 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 26–289（264 aa）
Not recorded BHU [[(2S)-2-methyl-3-sulfanyl-propanoyl]amino]methylboronic acid × 1 PEG DI(HYDROXYETHYL)ETHER × 2 ACY ACETIC ACID × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；32% to 35% PEG 8000, 0.1M lithium sulphate, 0.05M sodium acetate (pH 4.5)
Resolution 1.79 Å R-free 0.205
6J8Q Serine Beta-Lactamase KPC-2 in Complex with Dual MBL/SBL Inhibitor WL-001 Deposited 2019-01-21 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 26–289（264 aa）
Not recorded BHU [[(2S)-2-methyl-3-sulfanyl-propanoyl]amino]methylboronic acid × 1 PEG DI(HYDROXYETHYL)ETHER × 3 ACY ACETIC ACID × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；32% to 35% PEG 8000, 0.1M lithium sulphate, 0.05M sodium acetate (pH 4.5)
Resolution 1.79 Å R-free 0.205
6JN3 Serine Beta-Lactamase KPC-2 in Complex with Dual MBL/SBL Inhibitor MS05 Deposited 2019-03-13 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 26–289（264 aa）
Not recorded BX6 [(1R)-1-[[(2S)-2-methyl-3-sulfanyl-propanoyl]amino]-2-phenyl-ethyl]boronic acid × 1 PEG DI(HYDROXYETHYL)ETHER × 1 ACY ACETIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；32-35% PEG 8000, 0.1M lithium sulphate, 0.05M sodium acetate (pH 4.5)
Resolution 2.22 Å R-free 0.201
6JN3 Serine Beta-Lactamase KPC-2 in Complex with Dual MBL/SBL Inhibitor MS05 Deposited 2019-03-13 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 26–289（264 aa）
Not recorded BX6 [(1R)-1-[[(2S)-2-methyl-3-sulfanyl-propanoyl]amino]-2-phenyl-ethyl]boronic acid × 1 PEG DI(HYDROXYETHYL)ETHER × 3 ACY ACETIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；32-35% PEG 8000, 0.1M lithium sulphate, 0.05M sodium acetate (pH 4.5)
Resolution 2.22 Å R-free 0.201
6JN3 Serine Beta-Lactamase KPC-2 in Complex with Dual MBL/SBL Inhibitor MS05 Deposited 2019-03-13 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 26–289（264 aa）
Not recorded BX6 [(1R)-1-[[(2S)-2-methyl-3-sulfanyl-propanoyl]amino]-2-phenyl-ethyl]boronic acid × 1 PEG DI(HYDROXYETHYL)ETHER × 1 ACY ACETIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；32-35% PEG 8000, 0.1M lithium sulphate, 0.05M sodium acetate (pH 4.5)
Resolution 2.22 Å R-free 0.201
6JN3 Serine Beta-Lactamase KPC-2 in Complex with Dual MBL/SBL Inhibitor MS05 Deposited 2019-03-13 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 26–289（264 aa）
Not recorded BX6 [(1R)-1-[[(2S)-2-methyl-3-sulfanyl-propanoyl]amino]-2-phenyl-ethyl]boronic acid × 1 PEG DI(HYDROXYETHYL)ETHER × 1 ACY ACETIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；32-35% PEG 8000, 0.1M lithium sulphate, 0.05M sodium acetate (pH 4.5)
Resolution 2.22 Å R-free 0.201
6JN4 Serine Beta-Lactamase KPC-2 in Complex with Dual MBL/SBL Inhibitor WL-001 Deposited 2019-03-13 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 26–289（264 aa）
Not recorded BX9 [(R)-(4-fluorophenyl)-[[(2S)-2-methyl-3-sulfanyl-propanoyl]amino]methyl]boronic acid × 1 ACT ACETATE ION × 1 ACY ACETIC ACID × 2 PEG DI(HYDROXYETHYL)ETHER × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；0.1M Lithium Sulphate, 0.05M Sodium Acetate (pH 4.5), 32-35 % (v/v) Polyethylene glycol 8000
Resolution 1.90 Å R-free 0.221
6JN4 Serine Beta-Lactamase KPC-2 in Complex with Dual MBL/SBL Inhibitor WL-001 Deposited 2019-03-13 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 26–289（264 aa）
Not recorded BX9 [(R)-(4-fluorophenyl)-[[(2S)-2-methyl-3-sulfanyl-propanoyl]amino]methyl]boronic acid × 1 ACT ACETATE ION × 1 ACY ACETIC ACID × 1 PEG DI(HYDROXYETHYL)ETHER × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；0.1M Lithium Sulphate, 0.05M Sodium Acetate (pH 4.5), 32-35 % (v/v) Polyethylene glycol 8000
Resolution 1.90 Å R-free 0.221
6JN4 Serine Beta-Lactamase KPC-2 in Complex with Dual MBL/SBL Inhibitor WL-001 Deposited 2019-03-13 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 26–289（264 aa）
Not recorded BX9 [(R)-(4-fluorophenyl)-[[(2S)-2-methyl-3-sulfanyl-propanoyl]amino]methyl]boronic acid × 1 ACT ACETATE ION × 1 ACY ACETIC ACID × 1 PEG DI(HYDROXYETHYL)ETHER × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；0.1M Lithium Sulphate, 0.05M Sodium Acetate (pH 4.5), 32-35 % (v/v) Polyethylene glycol 8000
Resolution 1.90 Å R-free 0.221
6JN4 Serine Beta-Lactamase KPC-2 in Complex with Dual MBL/SBL Inhibitor WL-001 Deposited 2019-03-13 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 26–289（264 aa）
Not recorded BX9 [(R)-(4-fluorophenyl)-[[(2S)-2-methyl-3-sulfanyl-propanoyl]amino]methyl]boronic acid × 1 ACT ACETATE ION × 1 ACY ACETIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；0.1M Lithium Sulphate, 0.05M Sodium Acetate (pH 4.5), 32-35 % (v/v) Polyethylene glycol 8000
Resolution 1.90 Å R-free 0.221
7E9A Crystal structure of KPC-2 in complex with (S)-2-(1-hydroxy-1,3-dihydrobenzo[c][1,2]oxaborol-3-yl)acrylic acid (4a-(S)) Deposited 2021-03-03 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 26–289（264 aa）
Not recorded J00 2-[(3S)-1-oxidanyl-3H-2,1-benzoxaborol-3-yl]prop-2-enoic acid × 1 ACY ACETIC ACID × 1 PEG DI(HYDROXYETHYL)ETHER × 1 GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；32-35% PEG 8000, 0.1M lithium sulphate, 0.05M sodium acetate (pH 4.5)
Resolution 2.25 Å R-free 0.221
7E9A Crystal structure of KPC-2 in complex with (S)-2-(1-hydroxy-1,3-dihydrobenzo[c][1,2]oxaborol-3-yl)acrylic acid (4a-(S)) Deposited 2021-03-03 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 26–289（264 aa）
Not recorded J00 2-[(3S)-1-oxidanyl-3H-2,1-benzoxaborol-3-yl]prop-2-enoic acid × 1 PEG DI(HYDROXYETHYL)ETHER × 4 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；32-35% PEG 8000, 0.1M lithium sulphate, 0.05M sodium acetate (pH 4.5)
Resolution 2.25 Å R-free 0.221
7E9A Crystal structure of KPC-2 in complex with (S)-2-(1-hydroxy-1,3-dihydrobenzo[c][1,2]oxaborol-3-yl)acrylic acid (4a-(S)) Deposited 2021-03-03 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 26–289（264 aa）
Not recorded J00 2-[(3S)-1-oxidanyl-3H-2,1-benzoxaborol-3-yl]prop-2-enoic acid × 1 ACY ACETIC ACID × 1 PEG DI(HYDROXYETHYL)ETHER × 4 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；32-35% PEG 8000, 0.1M lithium sulphate, 0.05M sodium acetate (pH 4.5)
Resolution 2.25 Å R-free 0.221
7E9A Crystal structure of KPC-2 in complex with (S)-2-(1-hydroxy-1,3-dihydrobenzo[c][1,2]oxaborol-3-yl)acrylic acid (4a-(S)) Deposited 2021-03-03 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 26–289（264 aa）
Not recorded J00 2-[(3S)-1-oxidanyl-3H-2,1-benzoxaborol-3-yl]prop-2-enoic acid × 1 ACY ACETIC ACID × 1 PEG DI(HYDROXYETHYL)ETHER × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；32-35% PEG 8000, 0.1M lithium sulphate, 0.05M sodium acetate (pH 4.5)
Resolution 2.25 Å R-free 0.221
7LJK Crystal structure of the deacylation deficient KPC-2 F72Y mutant Deposited 2021-01-29 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 26–289（264 aa）
Mutation：F72Y No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；298 K；25% PEG 8,000, 0.1M KsCN, 0.1M Sodium Acetate pH:4.5
Resolution 1.81 Å R-free 0.197
7LJK Crystal structure of the deacylation deficient KPC-2 F72Y mutant Deposited 2021-01-29 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 26–289（264 aa）
Mutation：F72Y No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；298 K；25% PEG 8,000, 0.1M KsCN, 0.1M Sodium Acetate pH:4.5
Resolution 1.81 Å R-free 0.197
7LK8 Crystal structure of KPC-2 T215P mutant Deposited 2021-02-01 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 30–289（260 aa）
Mutation：T215P NA SODIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.15；298 K；2.5M NaCl, 0.1M Sodium Acetate pH:5.15
Resolution 1.43 Å R-free 0.186
7LK8 Crystal structure of KPC-2 T215P mutant Deposited 2021-02-01 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 30–289（260 aa）
Mutation：T215P NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.15；298 K；2.5M NaCl, 0.1M Sodium Acetate pH:5.15
Resolution 1.43 Å R-free 0.186

9 other PDB entries and 27 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q93LQ9_KLEPN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–264； UniProt 26–289 Author chain B； PDBConstruct 1–264； UniProt 26–289 Author chain C； PDBConstruct 1–264； UniProt 26–289 Author chain D； PDBConstruct 1–264； UniProt 26–289

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 6jn5

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6jn5
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6jn5
Deposition date deposition_date2019-03-13
Structure title titleSerine Beta-Lactamase KPC-2 in Complex with Dual MBL/SBL Inhibitor MS23
Keywords keywordsBeta-lactamase, Serine-beta-lactamase KPC-2, KPC-2, Carbapenemase, HYDROLASE; 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_guinier32.99 Å
Radius of gyration Rg (electron density) rg_electron32.51 Å
Forward intensity I(0) i0196087000.00
Molecular weight molecular_weight111950.0 kDa
Excluded volume excluded_volume139960 ų
Envelope volume envelope_volume166770 ų
Hydration-shell volume shell_volume42375 ų
Envelope diameter envelope_diameter109.0 Å
Shell Rg shell_rg39.55 Å
Envelope Rg envelope_rg32.48 Å
Shape Rg shape_rg32.50 Å
Total Rg total_rg33.06 Å
Total atoms total_atoms7891
Residues n_residues1049
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 dmax103.9 Å
Rg (real space) rg_real32.85 Å
Rg uncertainty (real space) rg_real_error0.70 Å
I(0) (real space) i0_real1.9610e+08
I(0) uncertainty (real space) i0_real_error3.3550e+06
Rg (reciprocal space) rg_reciprocal32.92 Å
I(0) (reciprocal space) i0_reciprocal196100000.0000
Solution quality estimate total_estimate0.9047
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary45.5 Å
Skewness Skewness skewness0.148
Kurtosis Kurtosis kurtosis-0.602
Angular range angular_range— – 0.2400 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha147400000.0000
Real-space data points n_real_points49
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.936; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.948
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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) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd6jn5a_
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.3 — beta-lactamase/transpeptidase-like
Superfamily Superfamily superfamilye.3.1 — beta-lactamase/transpeptidase-like
Family Family familye.3.1.0 — automated matches
Domain ID domain_idd6jn5b_
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.3 — beta-lactamase/transpeptidase-like
Superfamily Superfamily superfamilye.3.1 — beta-lactamase/transpeptidase-like
Family Family familye.3.1.0 — automated matches
Domain ID domain_idd6jn5c_
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.3 — beta-lactamase/transpeptidase-like
Superfamily Superfamily superfamilye.3.1 — beta-lactamase/transpeptidase-like
Family Family familye.3.1.0 — automated matches
Domain ID domain_idd6jn5d_
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.3 — beta-lactamase/transpeptidase-like
Superfamily Superfamily superfamilye.3.1 — beta-lactamase/transpeptidase-like
Family Family familye.3.1.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id6jn5A00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology710 — Beta-lactamase
Homologous superfamily homologous superfamily10 — DD-peptidase/beta-lactamase superfamily
Domain ID domain_id6jn5B00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology710 — Beta-lactamase
Homologous superfamily homologous superfamily10 — DD-peptidase/beta-lactamase superfamily
Domain ID domain_id6jn5C00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology710 — Beta-lactamase
Homologous superfamily homologous superfamily10 — DD-peptidase/beta-lactamase superfamily
Domain ID domain_id6jn5D00
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)