3sq5

Crystal Structure Analysis of the Yeast Tyrosyl-DNA Phosphodiesterase H432N Mutant

Method: X-RAY DIFFRACTION

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

Tyrosyl-DNA phosphodiesterase 1

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
5	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count
6	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TYDP1_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–462； UniProt 79–539 Author chain B； PDBConstruct 2–462； UniProt 79–539 Author chain C； PDBConstruct 2–462； UniProt 79–539 Author chain D； PDBConstruct 2–462； UniProt 79–539

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	3sq5
Deposition date deposition_date	2011-07-04
Structure title title	Crystal Structure Analysis of the Yeast Tyrosyl-DNA Phosphodiesterase H432N Mutant
Keywords keywords	Phosphodiesterase, DNA Binding, NUCLEAR, 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.

3sq5__assembly_1__model_1

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

Download this curve (.dat)

3sq5__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3sq5__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.38 Å
Rg (electron density)	21.17 Å
Total Rg	22.28 Å
Atom count	3415
Residues	419
Excluded volume	61518 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3sq5__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3sq5__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3sq5__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3sq5__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`3sq5__assembly_5__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`3sq5__assembly_6__model_1`	dimeric （2）	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 (2)

Entity 1 Entity 1 polymer

Description description	Tyrosyl-DNA phosphodiesterase 1
Molecular weight formula_weight	54028.0 kDa
EC 编号 ec_number	3.1.4.-
Mutation mutation	H432N
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	13812

MGAVFKLMKSDFYEREDFMGEVEDMITLKDIFGTETLKRSILFSFQYELDFLLRQFHQNVENITIVGQKGTIMPIEARAMDATLAVILKKVKLIEITMPPFASHHTKLIINFYDNGECKIFLPSNNFTSMETNLPQQVCWCSPLLKIGKEGLPVPFKRSLIEYLNSYHLKDIDELITKSVEEVNFAPLSELEFVYSTPSKFQSSGLLSFYNKLEKLSAGTSASDTAKHYLCQTSSIGTSLSRARDENLWTHLMIPLFTGIMSPPAKDTAGRKKAEILPTNSLINEYSQRKIKPYIIFPTEQEFVTSPLKWSSSGWFHFQYLQKKSYYEMLRNKFKVFYKQDPAMVTRRRGTTPANSKFYMHCATNSAGPCDASQVFKELEWCLYTSANLSQTAWGTVSRKPRNYEAGVLYHSRRLANTRKVTCRTFTRDRRGCAGNPTHVAVPFTLPVIPYDLAEDECFCLALHHHHHHH

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	125

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d3sq5a1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.136 — Phospholipase D/nuclease
Superfamily Superfamily superfamily	d.136.1 — Phospholipase D/nuclease
Family Family family	d.136.1.3 — Tyrosyl-DNA phosphodiesterase TDP1

Domain ID domain_id	d3sq5a2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.136 — Phospholipase D/nuclease
Superfamily Superfamily superfamily	d.136.1 — Phospholipase D/nuclease
Family Family family	d.136.1.3 — Tyrosyl-DNA phosphodiesterase TDP1

Domain ID domain_id	d3sq5b1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.136 — Phospholipase D/nuclease
Superfamily Superfamily superfamily	d.136.1 — Phospholipase D/nuclease
Family Family family	d.136.1.3 — Tyrosyl-DNA phosphodiesterase TDP1

Domain ID domain_id	d3sq5b2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.136 — Phospholipase D/nuclease
Superfamily Superfamily superfamily	d.136.1 — Phospholipase D/nuclease
Family Family family	d.136.1.3 — Tyrosyl-DNA phosphodiesterase TDP1

Domain ID domain_id	d3sq5c1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.136 — Phospholipase D/nuclease
Superfamily Superfamily superfamily	d.136.1 — Phospholipase D/nuclease
Family Family family	d.136.1.3 — Tyrosyl-DNA phosphodiesterase TDP1

Domain ID domain_id	d3sq5c2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.136 — Phospholipase D/nuclease
Superfamily Superfamily superfamily	d.136.1 — Phospholipase D/nuclease
Family Family family	d.136.1.3 — Tyrosyl-DNA phosphodiesterase TDP1

Domain ID domain_id	d3sq5d1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.136 — Phospholipase D/nuclease
Superfamily Superfamily superfamily	d.136.1 — Phospholipase D/nuclease
Family Family family	d.136.1.3 — Tyrosyl-DNA phosphodiesterase TDP1

Domain ID domain_id	d3sq5d2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.136 — Phospholipase D/nuclease
Superfamily Superfamily superfamily	d.136.1 — Phospholipase D/nuclease
Family Family family	d.136.1.3 — Tyrosyl-DNA phosphodiesterase TDP1

CATH v4.4 (8 domains)

Domain ID domain_id	3sq5A01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	870 — Endonuclease; Chain A
Homologous superfamily homologous superfamily	10 — Endonuclease Chain A

Domain ID domain_id	3sq5A02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	870 — Endonuclease; Chain A
Homologous superfamily homologous superfamily	10 — Endonuclease Chain A

Domain ID domain_id	3sq5B01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	870 — Endonuclease; Chain A
Homologous superfamily homologous superfamily	10 — Endonuclease Chain A

Domain ID domain_id	3sq5B02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	870 — Endonuclease; Chain A
Homologous superfamily homologous superfamily	10 — Endonuclease Chain A

Domain ID domain_id	3sq5C01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	870 — Endonuclease; Chain A
Homologous superfamily homologous superfamily	10 — Endonuclease Chain A

Domain ID domain_id	3sq5C02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	870 — Endonuclease; Chain A
Homologous superfamily homologous superfamily	10 — Endonuclease Chain A

Domain ID domain_id	3sq5D01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	870 — Endonuclease; Chain A
Homologous superfamily homologous superfamily	10 — Endonuclease Chain A

Domain ID domain_id	3sq5D02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	870 — Endonuclease; Chain A
Homologous superfamily homologous superfamily	10 — Endonuclease Chain A

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Unit-cell length a length_a	64.453 Å
Unit-cell length b length_b	82.036 Å
Unit-cell length c length_c	98.677 Å
Unit-cell angle α angle_alpha	89.80 °
Unit-cell angle β angle_beta	94.33 °
Unit-cell angle γ angle_gamma	112.78 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2040
R_work r_work	0.2030
R_free r_free	0.2360

Crystal Structure Analysis of the Yeast Tyrosyl-DNA Phosphodiesterase H432N Mutant

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

Tyrosyl-DNA phosphodiesterase 1

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

3sq5__assembly_1__model_1

3sq5__assembly_1__model_1 | I(q)

3sq5__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Crystal Structure Analysis of the Yeast Tyrosyl-DNA Phosphodiesterase H432N Mutant

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

Tyrosyl-DNA phosphodiesterase 1

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

3sq5__assembly_1__model_1

3sq5__assembly_1__model_1 | I(q)

3sq5__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)