SAXSdb — 8asc

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

X-ray repair cross-complementing protein 6

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 10 DNA 8	X-ray repair cross-complementing protein 5 × 4 （P13010） ;DNA (5'-D(PCPGPGPAPTPCPGPAPGPGPGPCPCPCPGPAPTPAPT)-3') ; × 4 ;DNA (5'-D(PGPGPGPCPCPCPTPCPGPAPTPCPCP*G)-3') ; × 4 Protein PAXX × 2 （Q9BUH6） SULFATE ION × 4 water × 7	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	XRCC6_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–544； UniProt 1–544 Author chain E； PDBConstruct 1–544； UniProt 1–544 Author chain K； PDBConstruct 1–544； UniProt 1–544 Author chain O； PDBConstruct 1–544； UniProt 1–544

X-ray repair cross-complementing protein 5

Homo sapiens

UniProt P13010

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 10 DNA 8	X-ray repair cross-complementing protein 6 × 4 （P12956） ;DNA (5'-D(PCPGPGPAPTPCPGPAPGPGPGPCPCPCPGPAPTPAPT)-3') ; × 4 ;DNA (5'-D(PGPGPGPCPCPCPTPCPGPAPTPCPCP*G)-3') ; × 4 Protein PAXX × 2 （Q9BUH6） SULFATE ION × 4 water × 7	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	XRCC5_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 19–572； UniProt 2–555 Author chain F； PDBConstruct 19–572； UniProt 2–555 Author chain L； PDBConstruct 19–572； UniProt 2–555 Author chain P； PDBConstruct 19–572； UniProt 2–555

Protein PAXX

OrganismNot specified

UniProt Q9BUH6

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 10 DNA 8	X-ray repair cross-complementing protein 6 × 4 （P12956） X-ray repair cross-complementing protein 5 × 4 （P13010） ;DNA (5'-D(PCPGPGPAPTPCPGPAPGPGPGPCPCPCPGPAPTPAPT)-3') ; × 4 ;DNA (5'-D(PGPGPGPCPCPCPTPCPGPAPTPCPCP*G)-3') ; × 4 SULFATE ION × 4 water × 7	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PAXX_HUMAN
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain J； PDBConstruct 1–28； UniProt 177–204 Author chain T； PDBConstruct 1–28； UniProt 177–204

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	8asc
Deposition date deposition_date	2022-08-19
Structure title title	Ku70/80 binds to the Ku-binding motif of PAXX
Keywords keywords	NHEJ, DNA repair, DNA BINDING PROTEIN; DNA BINDING PROTEIN
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.

8asc__assembly_1__model_1

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

Download this curve (.dat)

8asc__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8asc__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	76.99 Å
Rg (electron density)	78.19 Å
Total Rg	77.90 Å
Atom count	36363
Residues	4317
Excluded volume	643570 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8asc__assembly_1__model_1`	octadecameric （18）	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 (7)

Entity 1 Entity 1 polymer

Description description	X-ray repair cross-complementing protein 6
Molecular weight formula_weight	62629.6 kDa
EC 编号 ec_number	3.6.4.-,4.2.99.-
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,E,K,O
Atom count atom_count	36383

MSGWESYYKTEGDEEAEEEQEENLEASGDYKYSGRDSLIFLVDASKAMFESQSEDELTPFDMSIQCIQSVYISKIISSDRDLLAVVFYGTEKDKNSVNFKNIYVLQELDNPGAKRILELDQFKGQQGQKRFQDMMGHGSDYSLSEVLWVCANLFSDVQFKMSHKRIMLFTNEDNPHGNDSAKASRARTKAGDLRDTGIFLDLMHLKKPGGFDISLFYRDIISIAEDEDLRVHFEESSKLEDLLRKVRAKETRKRALSRLKLKLNKDIVISVGIYNLVQKALKPPPIKLYRETNEPVKTKTRTFNTSTGGLLLPSDTKRSQIYGSRQIILEKEETEELKRFDDPGLMLMGFKPLVLLKKHHYLRPSLFVYPEESLVIGSSTLFSALLIKCLEKEVAALCRYTPRRNIPPYFVALVPQEEELDDQKIQVTPPGFQLVFLPFADDKRKMPFTEKIMATPEQVGKMKAIVEKLRFTYRSDSFENPVLQQHFRNLEALALDLMEPEQAVDLTLPKVEAMNKRLGSLVDEFKELVYPPDYNPEGKVTKRK

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Spodoptera frugiperda

Entity 2 Entity 2 polymer

Description description	X-ray repair cross-complementing protein 5
Molecular weight formula_weight	65356.8 kDa
EC 编号 ec_number	3.6.4.-
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,F,L,P

MHHHHHHHHHHENLYFQGVRSGNKAAVVLCMDVGFTMSNSIPGIESPFEQAKKVITMFVQRQVFAENKDEIALVLFGTDGTDNPLSGGDQYQNITVHRHLMLPDFDLLEDIESKIQPGSQQADFLDALIVSMDVIQHETIGKKFEKRHIEIFTDLSSRFSKSQLDIIIHSLKKCDISLQFFLPFSLGKEDGSGDRGDGPFRLGGHGPSFPLKGITEQQKEGLEIVKMVMISLEGEDGLDEIYSFSESLRKLCVFKKIERHSIHWPCRLTIGSNLSIRIAAYKSILQERVKKTWTVVDAKTLKKEDIQKETVYCLNDDDETEVLKEDIIQGFRYGSDIVPFSKVDEEQMKYKSEGKCFSVLGFCKSSQVQRRFFMGNQVLKVFAARDDEAAAVALSSLIHALDDLDMVAIVRYAYDKRANPQVGVAFPHIKHNYECLVYVQLPFMEDLRQYMFSSLKNSKKYAPTEAQLNAVDALIDSMSLAKKDEKTDTLEDLFPTTKIPNPRFQRLFQCLLHRALHPREPLPPIQQHIWNMLNPPAEVTTKSQIPLSKIKTLFPLIEAKKKDQVTAQEIFQ

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Spodoptera frugiperda

Entity 3 Entity 3 polymer

Description description	;DNA (5'-D(PCPGPGPAPTPCPGPAPGPGPGPCPCPCPGPAPTPAP*T)-3') ;
Molecular weight formula_weight	9314.0 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C,G,M,Q

CGGATCGAGGGCCCGATATCTAGAGGGATC

Entity 4 Entity 4 polymer

Description description	;DNA (5'-D(PGPGPGPCPCPCPTPCPGPAPTPCPCPG)-3') ;
Molecular weight formula_weight	4546.9 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D,H,N,R

CGGGCCCTCGATCCG

Entity 5 Entity 5 polymer

Description description	Protein PAXX
Molecular weight formula_weight	3068.5 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	J,T

RRRCPGESLINPGFKSKKPAGGVDFDET

Entity 6 Entity 6 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 7 Entity 7 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) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	8ascB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	410 — von Willebrand factor, type A domain

Domain ID domain_id	8ascF01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	410 — von Willebrand factor, type A domain

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Unit-cell length a length_a	85.024 Å
Unit-cell length b length_b	428.570 Å
Unit-cell length c length_c	96.065 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.01 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	monoclinic

Resolution resolution	2.950 Å
Low-resolution limit resolution_low	45.320 Å
R factor r_factor	0.2547
R_work r_work	0.2520
R_free r_free	0.2981

Ku70/80 binds to the Ku-binding motif of PAXX

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

X-ray repair cross-complementing protein 6

State in the Current Structure

Other States of the Same Protein in the Database

X-ray repair cross-complementing protein 5

State in the Current Structure

Other States of the Same Protein in the Database

Protein PAXX

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

8asc__assembly_1__model_1

8asc__assembly_1__model_1 | I(q)

8asc__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 (7)

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 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Ku70/80 binds to the Ku-binding motif of PAXX

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

X-ray repair cross-complementing protein 6

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

X-ray repair cross-complementing protein 5

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Protein PAXX

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

8asc__assembly_1__model_1

8asc__assembly_1__model_1 | I(q)

8asc__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 (7)

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 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)