4kpe

Novel fluoroquinolones in complex with topoisomerase IV from S. pneumoniae and E-site G-gate

Method: X-RAY DIFFRACTION

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

DNA topoisomerase 4 subunit A

Streptococcus pneumoniae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 4 DNA 4	DNA topoisomerase 4 subunit B × 2 （Q59961） E-site DNA1 × 1 E-site DNA2 × 1 E-site DNA3 × 1 E-site DNA4 × 1 MAGNESIUM ION × 6 ;(7aR,8R)-8-amino-4-cyclopropyl-12-fluoro-1-oxo-4,7,7a,8,9,10-hexahydro-1H-pyrrolo[1',2':1,7]azepino[2,3-h]quinoline-2-carboxylic acid ; × 2 water × 4	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PARC_STRPN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–488； UniProt 1–488 Author chain B； PDBConstruct 1–488； UniProt 1–488

DNA topoisomerase 4 subunit B

Streptococcus pneumoniae serotype 4

UniProt Q59961

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 4 DNA 4	DNA topoisomerase 4 subunit A × 2 （P72525） E-site DNA1 × 1 E-site DNA2 × 1 E-site DNA3 × 1 E-site DNA4 × 1 MAGNESIUM ION × 6 ;(7aR,8R)-8-amino-4-cyclopropyl-12-fluoro-1-oxo-4,7,7a,8,9,10-hexahydro-1H-pyrrolo[1',2':1,7]azepino[2,3-h]quinoline-2-carboxylic acid ; × 2 water × 4	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PARE_STRPN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 25–268； UniProt 404–647 Author chain D； PDBConstruct 25–268； UniProt 404–647

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	4kpe
Deposition date deposition_date	2013-05-13
Structure title title	Novel fluoroquinolones in complex with topoisomerase IV from S. pneumoniae and E-site G-gate
Keywords keywords	PROTEIN-DNA CLEAVAGE COMPLEX, ISOMERASE-DNA-INHIBITOR COMPLEX, TOPOISOMERASE IIA, Quinolone, ACHN-245; ISOMERASE/DNA/INHIBITOR
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.

4kpe__assembly_1__model_1

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

Download this curve (.dat)

4kpe__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4kpe__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	36.51 Å
Rg (electron density)	36.57 Å
Total Rg	36.95 Å
Atom count	11216
Residues	1418
Excluded volume	196170 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4kpe__assembly_1__model_1`	octameric （8）	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 (9)

Entity 1 Entity 1 polymer

Description description	DNA topoisomerase 4 subunit A
Molecular weight formula_weight	56455.4 kDa
EC 编号 ec_number	5.99.1.3
Mutation mutation	I257T
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	11256

MSNIQNMSLEDIMGERFGRYSKYIIQDRALPDIRDGLKPVQRRILYSMNKDSNTFDKSYRKSAKSVGNIMGNFHPHGDSSIYDAMVRMSQNWKNREILVEMHGNNGSMDGDPPAAMRYTEARLSEIAGYLLQDIEKKTVPFAWNFDDTEKEPTVLPAAFPNLLVNGSTGISAGYATDIPPHNLAEVIDAAVYMIDHPTAKIDKLMEFLPGPDFPTGAIIQGRDEIKKAYETGKGRVVVRSKTEIEKLKGGKEQIVITEIPYEINKANLVKKIDDVRVNNKVAGIAEVRDESDRDGLRIAIELKKDANTELVLNYLFKYTDLQINYNFNMVAIDNFTPRQVGIVPILSSYIAHRREVILARSRFDKEKAEKRLHIVEGLIRVISILDEVIALIRASENKADAKENLKVSYDFTEEQAEAIVTLQLYRLTNTDVVVLQEEEAELREKIAMLAAIIGDERTMYNLMKKELREVKKKFATPRLSSLEDTAKALEHHHHHH

Source Source

Source organism organism	Streptococcus pneumoniae
NCBI taxonomy ID ncbi_taxonomy_id	170187
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	DNA topoisomerase 4 subunit B
Molecular weight formula_weight	30415.7 kDa
EC 编号 ec_number	5.99.1.3
Mutation mutation	V460I, T644A
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

MGHHHHHHHHHHSSGHIDDDDKHMKNKKDKGLLSGKLTPAQSKNPAKNELYLVEGDSAGGSAKQGRDRKFQAILPLRGKVINTAKAKMADILKNEEINTMIYTIGAGVGADFSIEDANYDKIIIMTDADTDGAHIQTLLLTFFYRYMRPLVEAGHVYIALPPLYKMSKGKGKKEEVAYAWTDGELEELRKQFGKGATLQRYKGLGEMNADQLWETTMNPETRTLIRVTIEDLARAERRVNVLMGDKVEPRRKWIEDNVKFTLEEATVF

Source Source

Source organism organism	Streptococcus pneumoniae serotype 4
NCBI taxonomy ID ncbi_taxonomy_id	170187
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	E-site DNA1
Molecular weight formula_weight	2121.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E

CATGAAT

Entity 4 Entity 4 polymer

Description description	E-site DNA2
Molecular weight formula_weight	3348.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	F

AGTCATTCATG

Entity 5 Entity 5 polymer

Description description	E-site DNA3
Molecular weight formula_weight	2113.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	G

CGTGCAT

Entity 6 Entity 6 polymer

Description description	E-site DNA4
Molecular weight formula_weight	3358.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	H

GACTATGCACG

Entity 7 Entity 7 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 8 Entity 8 non-polymer

Description description	;(7aR,8R)-8-amino-4-cyclopropyl-12-fluoro-1-oxo-4,7,7a,8,9,10-hexahydro-1H-pyrrolo[1',2':1,7]azepino[2,3-h]quinoline-2-carboxylic acid ;
Molecular weight formula_weight	369.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	24

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	4kpeC00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	670 —

Domain ID domain_id	4kpeD00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	670 —

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Unit-cell length a length_a	157.830 Å
Unit-cell length b length_b	157.830 Å
Unit-cell length c length_c	210.710 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	12

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	3.430 Å
Low-resolution limit resolution_low	41.819 Å
R factor r_factor	0.1562
R_work r_work	0.1541
R_free r_free	0.1947

Novel fluoroquinolones in complex with topoisomerase IV from S. pneumoniae and E-site G-gate

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

DNA topoisomerase 4 subunit A

State in the Current Structure

Other States of the Same Protein in the Database

DNA topoisomerase 4 subunit B

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

4kpe__assembly_1__model_1

4kpe__assembly_1__model_1 | I(q)

4kpe__assembly_1__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 (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 polymer

Polymer Polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Novel fluoroquinolones in complex with topoisomerase IV from S. pneumoniae and E-site G-gate

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

DNA topoisomerase 4 subunit A

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

DNA topoisomerase 4 subunit B

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

4kpe__assembly_1__model_1

4kpe__assembly_1__model_1 | I(q)

4kpe__assembly_1__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 (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 polymer

Polymer Polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)