SAXSdb — 2w3o

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

BIFUNCTIONAL POLYNUCLEOTIDE PHOSPHATASE/KINASE

HOMO SAPIENS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	DNA REPAIR PROTEIN XRCC1 × 1 （P18887） CALCIUM ION × 3 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	DNA REPAIR PROTEIN XRCC1 × 1 （P18887） CALCIUM ION × 3 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PNKP_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–113； UniProt 1–110 Author chain B； PDBConstruct 4–113； UniProt 1–110

DNA REPAIR PROTEIN XRCC1

OrganismNot specified

UniProt P18887

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	BIFUNCTIONAL POLYNUCLEOTIDE PHOSPHATASE/KINASE × 1 （Q96T60） CALCIUM ION × 3 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	BIFUNCTIONAL POLYNUCLEOTIDE PHOSPHATASE/KINASE × 1 （Q96T60） CALCIUM ION × 3 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	XRCC1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–8； UniProt 515–522 Author chain D； PDBConstruct 1–8； UniProt 515–522

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	2w3o
Deposition date deposition_date	2008-11-13
Structure title title	Crystal structure of the human PNKP FHA domain in complex with an XRCC1-derived phosphopeptide
Keywords keywords	;HYDROLASE, TRANSFERASE/PEPTIDE, FHA, PNKP, XRCC1, KINASE, NUCLEUS, POLYNUCLEOTIDE KINASE 3' PHOSPHATASE, DNA DAMAGE, DNA REPAIR, TRANSFERASE, ATP-BINDING, MULTIFUNCTIONAL ENZYME, POLYMORPHISM, PHOSPHOPROTEIN, PHOSPHO- PEPTIDE, NUCLEOTIDE-BINDING, BASE EXCISION REPAIR, TRANSFERASE-PEPTIDE complex ;; HYDROLASE,TRANSFERASE/PEPTIDE
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.

2w3o__assembly_1__model_1

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

Download this curve (.dat)

2w3o__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2w3o__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	14.64 Å
Rg (electron density)	13.22 Å
Total Rg	14.61 Å
Atom count	817
Residues	106
Excluded volume	14527 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2w3o__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2w3o__assembly_2__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 (4)

Entity 1 Entity 1 polymer

Description description	BIFUNCTIONAL POLYNUCLEOTIDE PHOSPHATASE/KINASE
Molecular weight formula_weight	12117.6 kDa
EC 编号 ec_number	3.1.3.32, 2.7.1.78
Mutation mutation	YES
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	1948

GPHMGEVEAPGRLWLESPPGEAPPIFLPSDGQALVLGRGPLTQVTDRKCSRTQVELVADPETRTVAVKQLGVNPSTTGTQELKPGLEGSLGVGDTLYLVNGEHPLTLRWEETR

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 2 Entity 2 polymer

Description description	DNA REPAIR PROTEIN XRCC1
Molecular weight formula_weight	1015.8 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

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

YAGSTDEN

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	286

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	2w3oA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	200 — Tumour Suppressor Smad4
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	2w3oB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	200 — Tumour Suppressor Smad4
Homologous superfamily homologous superfamily	20 —

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Unit-cell length a length_a	56.900 Å
Unit-cell length b length_b	56.900 Å
Unit-cell length c length_c	62.770 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	6

Space group space_group	P 3
Space-group number int_tables_number	143
Crystal system crystal_system	—

Resolution resolution	1.850 Å
Low-resolution limit resolution_low	62.750 Å
R factor r_factor	0.1810
R_work r_work	0.1780
R_free r_free	0.2360

Crystal structure of the human PNKP FHA domain in complex with an XRCC1-derived phosphopeptide

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

BIFUNCTIONAL POLYNUCLEOTIDE PHOSPHATASE/KINASE

State in the Current Structure

Other States of the Same Protein in the Database

DNA REPAIR PROTEIN XRCC1

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

2w3o__assembly_1__model_1

2w3o__assembly_1__model_1 | I(q)

2w3o__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of the human PNKP FHA domain in complex with an XRCC1-derived phosphopeptide

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

BIFUNCTIONAL POLYNUCLEOTIDE PHOSPHATASE/KINASE

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 REPAIR PROTEIN XRCC1

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

2w3o__assembly_1__model_1

2w3o__assembly_1__model_1 | I(q)

2w3o__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)