3l4k

Topoisomerase II-DNA cleavage complex, metal-bound

Method: X-RAY DIFFRACTION

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

DNA topoisomerase 2

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Monomer	Protein 1 DNA 4	;DNA (5'-D(PCPCPTPAPCPTPGPCPTPAPC)-3') ; × 1 ;DNA (5'-D(CPGPCPGPGPTPAPGPCPAPGPTPAPGPG)-3') ; × 1 ;DNA (5'-D(PGPGPAPTPGPAPCPGPAPTP)-3') ; × 1 ;DNA (5'-D(CPGPCPGPAPAPTPCPGPTPCPAPTPCPC)-3') ; × 1 ZINC ION × 8 3'-THIO-THYMIDINE-5'-PHOSPHATE × 1 water × 3	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TOP2_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–757； UniProt 421–1177

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	3l4k
Deposition date deposition_date	2009-12-20
Structure title title	Topoisomerase II-DNA cleavage complex, metal-bound
Keywords keywords	;TOPOISOMERASE, PROTEIN-DNA COMPLEX, COVALENTLY LINKED COMPLEX, DNA SUPERCOILING, DNA REPLICATION, ATP-binding, DNA-binding, Isomerase, Nucleotide-binding, Nucleus, Phosphoprotein, Isomerase-DNA complex ;; Isomerase/DNA
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.

3l4k__assembly_1__model_1

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

Download this curve (.dat)

3l4k__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3l4k__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.57 Å
Rg (electron density)	31.68 Å
Total Rg	32.17 Å
Atom count	6466
Residues	746
Excluded volume	114350 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3l4k__assembly_1__model_1`	pentameric （5）	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 (8)

Entity 1 Entity 1 polymer

Description description	DNA topoisomerase 2
Molecular weight formula_weight	88025.2 kDa
EC 编号 ec_number	5.99.1.3
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	7028

SRITNYPKLEDANKAGTKEGYKCTLVLTEGDSALSLAVAGLAVVGRDYYGCYPLRGKMLNVREASADQILKNAEIQAIKKIMGLQHRKKYEDTKSLRYGHLMIMTDQDHDGSHIKGLIINFLESSFPGLLDIQGFLLEFITPIIKVSITKPTKNTIAFYNMPDYEKWREEESHKFTWKQKYYKGLGTSLAQEVREYFSNLDRHLKIFHSLQGNDKDYIDLAFSKKKADDRKEWLRQYEPGTVLDPTLKEIPISDFINKELILFSLADNIRSIPNVLDGFKPGQRKVLYGCFKKNLKSELKVAQLAPYVSECTAYHHGEQSLAQTIIGLAQNFVGSNNIYLLLPNGAFGTRATGGKDAAAARYIYTELNKLTRKIFHPADDPLYKYIQEDEKTVEPEWYLPILPMILVNGAEGIGTGWSTYIPPFNPLEIIKNIRHLMNDEELEQMHPWFRGWTGTIEEIEPLRYRMYGRIEQIGDNVLEITELPARTWTSTIKEYLLLGLSGNDKIKPWIKDMEEQHDDNIKFIITLSPEEMAKTRKIGFYERFKLISPISLMNMVAFDPHGKIKKYNSVNEILSEFYYVRLEYYQKRKDHMSERLQWEVEKYSFQVKFIKMIIEKELTVTNKPRNAIIQELENLGFPRFNKEGKPYYGSPNDEIAEQINDVKGATSDEEDEESSHEDTENVINGPEELYGTYEYLLGMRIWSLTKERYQKLLKQKQEKETELENLLKLSAKDIWNTDLKAFEVGYQEFLQRDAEAR

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;brewer's yeast,lager beer yeast,yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	SACCHAROMYCES CEREVISIAE

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(PCPCPTPAPCPTPGPCPTPAP*C)-3') ;
Molecular weight formula_weight	3269.1 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	B

CCTACTGCTAC

Entity 3 Entity 3 polymer

Description description	;DNA (5'-D(CPGPCPGPGPTPAPGPCPAPGPTPAPGP*G)-3') ;
Molecular weight formula_weight	4675.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C

CGCGGTAGCAGTAGG

Entity 4 Entity 4 polymer

Description description	;DNA (5'-D(PGPGPAPTPGPAPCPGPAPTP*)-3') ;
Molecular weight formula_weight	3109.1 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D

GGATGACGAT

Entity 5 Entity 5 polymer

Description description	;DNA (5'-D(CPGPCPGPAPAPTPCPGPTPCPAPTPCP*C)-3') ;
Molecular weight formula_weight	4529.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E

CGCGAATCGTCATCC

Entity 6 Entity 6 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 7 Entity 7 non-polymer

Description description	3'-THIO-THYMIDINE-5'-PHOSPHATE
Molecular weight formula_weight	338.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	20

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3l4ka_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.11 — Type II DNA topoisomerase C-terminal domain-like
Superfamily Superfamily superfamily	e.11.1 — Type II DNA topoisomerase C-terminal domain-like
Family Family family	e.11.1.1 — Type II DNA topoisomerase C-terminal domain-like

CATH v4.4 (5 domains)

Domain ID domain_id	3l4kA01
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	3l4kA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	3l4kA03
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	199 — Topoisomerase II; domain 5
Homologous superfamily homologous superfamily	10 — Topoisomerase II, domain 5

Domain ID domain_id	3l4kA04
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	3l4kA05
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	268 — Topoisomerase; domain 3
Homologous superfamily homologous superfamily	10 — Topoisomerase, domain 3

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Unit-cell length a length_a	86.064 Å
Unit-cell length b length_b	91.851 Å
Unit-cell length c length_c	115.939 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 2 21
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.980 Å
Low-resolution limit resolution_low	49.023 Å
R factor r_factor	0.2408
R_work r_work	0.2391
R_free r_free	0.2733

Topoisomerase II-DNA cleavage complex, metal-bound

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

DNA topoisomerase 2

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

3l4k__assembly_1__model_1

3l4k__assembly_1__model_1 | I(q)

3l4k__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

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 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (1 domains)

CATH v4.4 (5 domains)

7. Citations (1)

Topoisomerase II-DNA cleavage complex, metal-bound

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

DNA topoisomerase 2

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

3l4k__assembly_1__model_1

3l4k__assembly_1__model_1 | I(q)

3l4k__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

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 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (1 domains)

CATH v4.4 (5 domains)

7. Citations (1)