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6k0r

Ruvbl1-Ruvbl2 with truncated domain II in complex with phosphorylated Cordycepin

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

RuvB-like 1,RuvB-like 1

Homo sapiens

UniProt Q9Y265

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 6 RuvB-like 2,RuvB-like 2 × 3 （Q9Y230） ADENOSINE-5'-DIPHOSPHATE × 1 [(2~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-oxolan-2-yl]methyl phosphono hydrogen phosphate × 4 MAGNESIUM ION × 1 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE × 1 water × 3 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 6 RuvB-like 2,RuvB-like 2 × 3 （Q9Y230） [(2~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-oxolan-2-yl]methyl phosphono hydrogen phosphate × 4 MAGNESIUM ION × 1 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE × 1 [(2~{R},3~{S},4~{S})-3,4-bis(oxidanyl)oxolan-2-yl]methyl phosphono hydrogen phosphate × 1 water × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers
2c9o 2c9o

2 assemblies

Heteromeric or nucleic-acid complex
2xsz 5oaf 6fo1 6hts 6igm 6k0r 6k0r 6qi8 6qi9 7aho 7ole 7p6x

36 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name RUVB1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 4–128； UniProt 2–126 Author chain A； PDBConstruct 133–355； UniProt 234–456 Author chain B； PDBConstruct 4–128； UniProt 2–126 Author chain B； PDBConstruct 133–355； UniProt 234–456 Author chain C； PDBConstruct 4–128； UniProt 2–126 Author chain C； PDBConstruct 133–355； UniProt 234–456 Author chain G； PDBConstruct 4–128； UniProt 2–126 Author chain G； PDBConstruct 133–355； UniProt 234–456 Author chain H； PDBConstruct 4–128； UniProt 2–126 Author chain H； PDBConstruct 133–355； UniProt 234–456 Author chain I； PDBConstruct 4–128； UniProt 2–126 Author chain I； PDBConstruct 133–355； UniProt 234–456

RuvB-like 2,RuvB-like 2

Homo sapiens

UniProt Q9Y230

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 6 RuvB-like 1,RuvB-like 1 × 3 （Q9Y265） ADENOSINE-5'-DIPHOSPHATE × 1 [(2~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-oxolan-2-yl]methyl phosphono hydrogen phosphate × 4 MAGNESIUM ION × 1 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE × 1 water × 3 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 6 RuvB-like 1,RuvB-like 1 × 3 （Q9Y265） [(2~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-oxolan-2-yl]methyl phosphono hydrogen phosphate × 4 MAGNESIUM ION × 1 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE × 1 [(2~{R},3~{S},4~{S})-3,4-bis(oxidanyl)oxolan-2-yl]methyl phosphono hydrogen phosphate × 1 water × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
2cqa

1 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers
3uk6 3uk6 6h7x

3 assemblies

Heteromeric or nucleic-acid complex
2xsz 5oaf 6fo1 6hts 6igm 6k0r 6k0r 6qi8 6qi9 7aho 7ole 7p6x

36 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name RUVB2_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain D； PDBConstruct 4–136； UniProt 1–133 Author chain D； PDBConstruct 141–366； UniProt 238–463 Author chain E； PDBConstruct 4–136； UniProt 1–133 Author chain E； PDBConstruct 141–366； UniProt 238–463 Author chain F； PDBConstruct 4–136； UniProt 1–133 Author chain F； PDBConstruct 141–366； UniProt 238–463 Author chain J； PDBConstruct 4–136； UniProt 1–133 Author chain J； PDBConstruct 141–366； UniProt 238–463 Author chain K； PDBConstruct 4–136； UniProt 1–133 Author chain K； PDBConstruct 141–366； UniProt 238–463 Author chain L； PDBConstruct 4–136； UniProt 1–133 Author chain L； PDBConstruct 141–366； UniProt 238–463

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_id6k0r
Deposition date deposition_date2019-05-07
Structure title titleRuvbl1-Ruvbl2 with truncated domain II in complex with phosphorylated Cordycepin
Keywords keywordsATPase, Cordycepin, CIRCADIAN CLOCK PROTEIN; CIRCADIAN CLOCK PROTEIN
Experimental Method methodX-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.

6k0r__assembly_1__model_1

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

Download this curve (.dat)

6k0r__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

6k0r__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）40.91 Å
Rg (electron density)40.08 Å
Total Rg40.48 Å
Atom count13759
Residues1861
Excluded volume244680 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 6k0r__assembly_1__model_1 hexameric （6） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 6k0r__assembly_2__model_1 hexameric （6） 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 (8)

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6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id6k0rA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id6k0rA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily60 —
Domain ID domain_id6k0rB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id6k0rB02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily60 —
Domain ID domain_id6k0rC01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id6k0rC02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily60 —
Domain ID domain_id6k0rG01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id6k0rG02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily60 —
Domain ID domain_id6k0rH01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id6k0rH02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily60 —
Domain ID domain_id6k0rI01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id6k0rI02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily60 —
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7. Citations (1)