SAXSdb — 1rff

▼

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

Tyrosyl-DNA phosphodiesterase 1

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 2 DNA 1	5'-D(APGPTPT)-3' × 1 Topoisomerase I-Derived Peptide × 1 VANADATE ION × 1 SPERMINE × 1 water × 3	Consistent with all polymers
2	Protein–DNA	Heteromer	Protein 2 DNA 1	5'-D(APGPTPT)-3' × 1 Topoisomerase I-Derived Peptide × 1 VANADATE ION × 1 SPERMINE × 1 water × 3	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TYDP1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 26–485； UniProt 149–608 Author chain B； PDBConstruct 26–485； UniProt 149–608

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	1rff
Deposition date deposition_date	2003-11-08
Structure title title	Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, octapeptide KLNYYDPR, and tetranucleotide AGTT.
Keywords keywords	Protein-DNA complex, vanadate complex, transition state mimic, HYDROLASE-DNA COMPLEX; HYDROLASE/DNA
Experimental Method method	X-RAY DIFFRACTION

▼

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.

1rff__assembly_1__model_1

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

Download this curve (.dat)

1rff__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1rff__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.91 Å
Rg (electron density)	20.69 Å
Total Rg	21.71 Å
Atom count	3518
Residues	434
Excluded volume	62882 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1rff__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1rff__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	5'-D(APGPTPT)-3'
Molecular weight formula_weight	1205.8 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D,F
Atom count atom_count	7412

AGTT

Entity 2 Entity 2 polymer

Description description	Tyrosyl-DNA phosphodiesterase 1
Molecular weight formula_weight	54731.2 kDa
EC 编号 ec_number	3.1.4.-
Mutation mutation	D322N, M328T, F548L
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B

MGSSHHHHHHSSGLVPRGSHMLEDPGEGQDIWDMLDKGNPFQFYLTRVSGVKPKYNSGALHIKDILSPLFGTLVSSAQFNYCFDVDWLVKQYPPEFRKKPILLVHGDKREAKAHLHAQAKPYENISLCQAKLDIAFGTHHTKMMLLLYEEGLRVVIHTSNLIHADWHQKTQGIWLSPLYPRIADGTHKSGESPTHFKANLISYLTAYNAPSLKEWIDVIHKHDLSETNVYLIGSTPGRFQGSQKDNWGHFRLKKLLKDHASSMPNAESWPVVGQFSSVGSLGADESKWLCSEFKESMLTLGKESKTPGKSSVPLYLIYPSVENVRTSLEGYPAGGSLPYSIQTAEKQNWLHSYFHKWSAETSGRSNAMPHIKTYMRPSPDFSKIAWFLVTSANLSKAAWGALEKNGTQLMIRSYELGVLFLPSALGLDSFKVKQKFFAGSQEPMATFPVPYDLPPELYGSKDRPWIWNIPYVKAPDTHGNMWVPS

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Topoisomerase I-Derived Peptide
Molecular weight formula_weight	1070.2 kDa
Mutation mutation	L724Y
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

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

KLNYYDPR

Entity 4 Entity 4 non-polymer

Description description	VANADATE ION
Molecular weight formula_weight	114.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	SPERMINE
Molecular weight formula_weight	202.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	343

▼

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1rffa1
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	d1rffa2
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	d1rffb1
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	d1rffb2
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 (4 domains)

Domain ID domain_id	1rffA01
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	1rffA02
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	1rffB01
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	1rffB02
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

▶

Unit-cell length a length_a	50.076 Å
Unit-cell length b length_b	104.904 Å
Unit-cell length c length_c	193.832 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	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.1936
R_work r_work	0.1926
R_free r_free	0.2132

Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, octapeptide KLNYYDPR, and tetranucleotide AGTT.

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

1rff__assembly_1__model_1

1rff__assembly_1__model_1 | I(q)

1rff__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (4)

Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, octapeptide KLNYYDPR, and tetranucleotide AGTT.

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

1rff__assembly_1__model_1

1rff__assembly_1__model_1 | I(q)

1rff__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (4)