SAXSdb — 6erh

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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 3 DNA 2	X-ray repair cross-complementing protein 5 × 1 （P13010） DNA (34-MER) × 1 DNA (21-MER) × 1 Non-homologous end-joining factor 1 × 1 （Q9H9Q4） SULFATE ION × 1 water × 3	Consistent with all polymers
2	Protein–DNA	Heteromer	Protein 3 DNA 2	X-ray repair cross-complementing protein 5 × 1 （P13010） DNA (34-MER) × 1 DNA (21-MER) × 1 Non-homologous end-joining factor 1 × 1 （Q9H9Q4） SULFATE ION × 1 water × 4	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 C； 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 3 DNA 2	X-ray repair cross-complementing protein 6 × 1 （P12956） DNA (34-MER) × 1 DNA (21-MER) × 1 Non-homologous end-joining factor 1 × 1 （Q9H9Q4） SULFATE ION × 1 water × 3	Consistent with all polymers
2	Protein–DNA	Heteromer	Protein 3 DNA 2	X-ray repair cross-complementing protein 6 × 1 （P12956） DNA (34-MER) × 1 DNA (21-MER) × 1 Non-homologous end-joining factor 1 × 1 （Q9H9Q4） SULFATE ION × 1 water × 4	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 D； PDBConstruct 19–572； UniProt 2–555

Non-homologous end-joining factor 1

OrganismNot specified

UniProt Q9H9Q4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 3 DNA 2	X-ray repair cross-complementing protein 6 × 1 （P12956） X-ray repair cross-complementing protein 5 × 1 （P13010） DNA (34-MER) × 1 DNA (21-MER) × 1 SULFATE ION × 1 water × 3	Consistent with all polymers
2	Protein–DNA	Heteromer	Protein 3 DNA 2	X-ray repair cross-complementing protein 6 × 1 （P12956） X-ray repair cross-complementing protein 5 × 1 （P13010） DNA (34-MER) × 1 DNA (21-MER) × 1 SULFATE ION × 1 water × 4	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NHEJ1_HUMAN
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain M； PDBConstruct 1–19； UniProt 281–299 Author chain T； PDBConstruct 1–19； UniProt 281–299

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	6erh
Deposition date deposition_date	2017-10-18
Structure title title	Complex of XLF and heterodimer Ku bound to DNA
Keywords keywords	DNA repair complex NHEJ, 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.

6erh__assembly_1__model_1

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

Download this curve (.dat)

6erh__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6erh__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	35.37 Å
Rg (electron density)	35.07 Å
Total Rg	35.48 Å
Atom count	9394
Residues	1084
Excluded volume	164990 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6erh__assembly_1__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6erh__assembly_2__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 (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	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	18810

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	2

Polymer Polymer

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

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 (34-MER)
Molecular weight formula_weight	10325.7 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	F,O

CGCGCCCAGCTTTCCCAGCTAATAAACTAAAAAC

Entity 4 Entity 4 polymer

Description description	DNA (21-MER)
Molecular weight formula_weight	6506.2 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	K,R

GTTTTTAGTTTATTGGGCGCG

Entity 5 Entity 5 polymer

Description description	Non-homologous end-joining factor 1
Molecular weight formula_weight	2273.8 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

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

LQRPQLSKVKRKKPRGLFS

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	2

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	33

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6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id	6erhA01
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	6erhA02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	290 — Ku70; Chain: A; Domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	6erhA03
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	970 — Ku70, bridge and pillars
Homologous superfamily homologous superfamily	10 — Ku70, bridge and pillars

Domain ID domain_id	6erhA04
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1600 — Ku70; Chain: A; domain 4
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	6erhB01
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	6erhB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1600 — Ku70; Chain: A; domain 4
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	6erhC01
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	6erhC02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	290 — Ku70; Chain: A; Domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	6erhC03
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	970 — Ku70, bridge and pillars
Homologous superfamily homologous superfamily	10 — Ku70, bridge and pillars

Domain ID domain_id	6erhC04
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1600 — Ku70; Chain: A; domain 4
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	6erhD01
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	6erhD02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1600 — Ku70; Chain: A; domain 4
Homologous superfamily homologous superfamily	10 —

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Unit-cell length a length_a	111.847 Å
Unit-cell length b length_b	118.925 Å
Unit-cell length c length_c	128.219 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	93.11 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	49.380 Å
R factor r_factor	0.2260
R_work r_work	0.2250
R_free r_free	0.2520

Complex of XLF and heterodimer Ku bound to DNA

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

Non-homologous end-joining factor 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

6erh__assembly_1__model_1

6erh__assembly_1__model_1 | I(q)

6erh__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) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)

Complex of XLF and heterodimer Ku bound to DNA

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

Non-homologous end-joining factor 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

6erh__assembly_1__model_1

6erh__assembly_1__model_1 | I(q)

6erh__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) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)