9EMA

RUVBL1/2 in complex with ATP and CB-6644 inhibitor

PDB DOI: https://doi.org/10.2210/pdb9EMA/pdb
EM Map EMD-19815: EMDB EMDataResource

Classification: CHAPERONE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-03-07 Released: 2024-05-15
Deposition Author(s): Lopez-Perrote, A., Llorca, O., Garcia-Martin, C.
Funding Organization(s): Agencia Estatal de Investigacion (AEI)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.40 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Mechanism of allosteric inhibition of RUVBL1-RUVBL2 by the small-molecule CB-6644

Garcia-Martin, C., Lopez-Perrote, A., Boskovic, J., Llorca, O.

(2024) Cell Rep Phys Sci

DOI: https://doi.org/10.1016/j.xcrp.2024.101982

Macromolecule Content

Total Structure Weight: 411.9 kDa
Atom Count: 15,562
Modelled Residue Count: 1,974
Deposited Residue Count: 3,669
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RuvB-like 1	A, B, C	459	Homo sapiens	Mutation(s): 0 Gene Names: RUVBL1, INO80H, NMP238, TIP49, TIP49A EC: 3.6.4.12
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y265 (Homo sapiens) Explore Q9Y265 Go to UniProtKB: Q9Y265
PHAROS: Q9Y265 GTEx: ENSG00000175792
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9Y265
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RuvB-like 2	D, E, F	764	Homo sapiens	Mutation(s): 0 Gene Names: RUVBL2, INO80J, TIP48, TIP49B, CGI-46 EC: 3.6.4.12
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y230 (Homo sapiens) Explore Q9Y230 Go to UniProtKB: Q9Y230
PHAROS: Q9Y230 GTEx: ENSG00000183207
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9Y230
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1H5V (Subject of Investigation/LOI) Query on A1H5V Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain L [auth C] SDF format, chain J [auth B] MOL2 format, chain H [auth A] MOL2 format, chain L [auth C] MOL2 format, chain J [auth B]	H [auth A], J [auth B], L [auth C]	5-chloranyl-2-ethoxy-4-fluoranyl-~{N}-[4-[[3-(methoxymethyl)-1-oxidanylidene-6,7-dihydro-5~{H}-pyrazolo[1,2-a][1,2]benzodiazepin-2-yl]amino]-2,2-dimethyl-4-oxidanylidene-butyl]benzamide C₂₉ H₃₄ Cl F N₄ O₅ VYCOZEBCSAQCES-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth C] Interactions & Density Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth C]
ATP Query on ATP Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain M [auth D] SDF format, chain R [auth F] SDF format, chain G [auth A] SDF format, chain K [auth C] SDF format, chain O [auth E] MOL2 format, chain I [auth B] MOL2 format, chain M [auth D] MOL2 format, chain R [auth F] MOL2 format, chain G [auth A] MOL2 format, chain K [auth C] MOL2 format, chain O [auth E]	G [auth A] I [auth B] K [auth C] M [auth D] O [auth E] G [auth A], I [auth B], K [auth C], M [auth D], O [auth E], R [auth F]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain O [auth E] Focus chain R [auth F] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain O [auth E] Focus chain R [auth F]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain N [auth D] SDF format, chain S [auth F] SDF format, chain P [auth E] SDF format, chain Q [auth F] MOL2 format, chain N [auth D] MOL2 format, chain S [auth F] MOL2 format, chain P [auth E] MOL2 format, chain Q [auth F]	N [auth D], P [auth E], Q [auth F], S [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain N [auth D] Focus chain P [auth E] Focus chain Q [auth F] Focus chain S [auth F] Interactions & Density Focus chain N [auth D] Focus chain P [auth E] Focus chain Q [auth F] Focus chain S [auth F]