SAXSdb — 7e9a

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

Beta-lactamase

Klebsiella pneumoniae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	2-[(3S)-1-oxidanyl-3H-2,1-benzoxaborol-3-yl]prop-2-enoic acid × 1 ACETIC ACID × 1 DI(HYDROXYETHYL)ETHER × 1 GLYCEROL × 3 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	2-[(3S)-1-oxidanyl-3H-2,1-benzoxaborol-3-yl]prop-2-enoic acid × 1 DI(HYDROXYETHYL)ETHER × 4 GLYCEROL × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	2-[(3S)-1-oxidanyl-3H-2,1-benzoxaborol-3-yl]prop-2-enoic acid × 1 ACETIC ACID × 1 DI(HYDROXYETHYL)ETHER × 4 GLYCEROL × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	2-[(3S)-1-oxidanyl-3H-2,1-benzoxaborol-3-yl]prop-2-enoic acid × 1 ACETIC ACID × 1 DI(HYDROXYETHYL)ETHER × 1 GLYCEROL × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	7e9a
Deposition date deposition_date	2021-03-03
Structure title title	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))
Keywords keywords	Beta-lactamase, Serine-beta-lactamase KPC-2, KPC-2, Carbapenemase, HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

7e9a__assembly_4__model_1

Assembly 4 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

7e9a__assembly_4__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7e9a__assembly_4__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	18.38 Å
Rg (electron density)	17.30 Å
Total Rg	18.27 Å
Atom count	1987
Residues	263
Excluded volume	35191 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7e9a__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`7e9a__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`7e9a__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`7e9a__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Beta-lactamase
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	8391

STNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLG

Source Source

Source organism organism	Klebsiella pneumoniae
NCBI taxonomy ID ncbi_taxonomy_id	573
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	2-[(3S)-1-oxidanyl-3H-2,1-benzoxaborol-3-yl]prop-2-enoic acid
Molecular weight formula_weight	204.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	ACETIC ACID
Molecular weight formula_weight	60.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	368

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	7e9aA01
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	7e9aB01
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	7e9aC01
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	7e9aD01
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

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Unit-cell length a length_a	165.421 Å
Unit-cell length b length_b	165.421 Å
Unit-cell length c length_c	94.860 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	2.250 Å
Low-resolution limit resolution_low	47.430 Å
R factor r_factor	0.1816
R_work r_work	0.1804
R_free r_free	0.2210

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))

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

7e9a__assembly_4__model_1

7e9a__assembly_4__model_1 | I(q)

7e9a__assembly_4__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

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))

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

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

7e9a__assembly_4__model_1

7e9a__assembly_4__model_1 | I(q)

7e9a__assembly_4__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)