SAXSdb — 6jn3

▼

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

Serine Beta-Lactamase KPC-2

Klebsiella pneumoniae

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	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
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 26–289	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
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 26–289	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
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 26–289	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

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 6JN3	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
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
6JN5 Serine Beta-Lactamase KPC-2 in Complex with Dual MBL/SBL Inhibitor MS23 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	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
6JN5 Serine Beta-Lactamase KPC-2 in Complex with Dual MBL/SBL Inhibitor MS23 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	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
6JN5 Serine Beta-Lactamase KPC-2 in Complex with Dual MBL/SBL Inhibitor MS23 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	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
6JN5 Serine Beta-Lactamase KPC-2 in Complex with Dual MBL/SBL Inhibitor MS23 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	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
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 2–265； UniProt 26–289 Author chain B； PDBConstruct 2–265； UniProt 26–289 Author chain C； PDBConstruct 2–265； UniProt 26–289 Author chain D； PDBConstruct 2–265； 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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	6jn3
Deposition date deposition_date	2019-03-13
Structure title title	Serine Beta-Lactamase KPC-2 in Complex with Dual MBL/SBL Inhibitor MS05
Keywords keywords	Beta-lactamase, Serine-beta-lactamase KPC-2, KPC-2, Carbapenemase, HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	33.07 Å
Radius of gyration Rg (electron density) rg_electron	32.60 Å
Forward intensity I(0) i0	200880000.00
Molecular weight molecular_weight	113490.0 kDa
Excluded volume excluded_volume	142000 Å³
Envelope volume envelope_volume	170860 Å³
Hydration-shell volume shell_volume	43173 Å³
Envelope diameter envelope_diameter	109.6 Å
Shell Rg shell_rg	39.66 Å
Envelope Rg envelope_rg	32.75 Å
Shape Rg shape_rg	32.59 Å
Total Rg total_rg	33.18 Å
Total atoms total_atoms	7996
Residues n_residues	1054
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	104.1 Å
Rg (real space) rg_real	32.93 Å
Rg uncertainty (real space) rg_real_error	0.69 Å
I(0) (real space) i0_real	2.0090e+08
I(0) uncertainty (real space) i0_real_error	2.8950e+06
Rg (reciprocal space) rg_reciprocal	33.00 Å
I(0) (reciprocal space) i0_reciprocal	200900000.0000
Solution quality estimate total_estimate	0.9045
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	45.6 Å
Skewness Skewness skewness	0.162
Kurtosis Kurtosis kurtosis	-0.590
Angular range angular_range	— – 0.2400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	159200000.0000
Real-space data points n_real_points	49
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.938; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.940

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Serine Beta-Lactamase KPC-2
Molecular weight formula_weight	28079.6 kDa
EC 编号 ec_number	3.5.2.6
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	8559

STNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLG

来源 Source

来源生物 organism	Klebsiella pneumoniae
NCBI Class编号 ncbi_taxonomy_id	573
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	[(1R)-1-[[(2S)-2-methyl-3-sulfanyl-propanoyl]amino]-2-phenyl-ethyl]boronic acid
Molecular weight formula_weight	267.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	ACETIC ACID
Molecular weight formula_weight	60.1 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	551

▼

7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d6jn3a1
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.3.1.0 — automated matches

Domain ID domain_id	d6jn3a2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d6jn3b_
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.3.1.0 — automated matches

Domain ID domain_id	d6jn3c1
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.3.1.0 — automated matches

Domain ID domain_id	d6jn3c2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d6jn3d_
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.3.1.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id	6jn3A00
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

Domain ID domain_id	6jn3B00
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

Domain ID domain_id	6jn3C00
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

Domain ID domain_id	6jn3D00
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	165.515 Å
Unit-cell length b length_b	165.515 Å
Unit-cell length c length_c	94.681 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	P 3 2 1
Space-group number int_tables_number	150
Crystal system crystal_system	—

Resolution resolution	2.216 Å
Low-resolution limit resolution_low	47.780 Å
R factor r_factor	0.1675
R_work r_work	0.1668
R_free r_free	0.2011

fit	/app/data/saxs_computation/jn/6jn3/6jn3.fit
pddf	/app/data/pr_computation/jn/6jn3/6jn3.pr.out
profile	/app/data/saxs_computation/jn/6jn3/6jn3.dat

Serine Beta-Lactamase KPC-2 in Complex with Dual MBL/SBL Inhibitor MS05

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

Serine Beta-Lactamase KPC-2

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

Diffraction experiment Diffraction