8R7E | pdb_00008r7e

MutSbeta bound to compound CHDI-00898647 in the canonical DNA-mismatch bound form

PDB DOI: https://doi.org/10.2210/pdb8R7E/pdb
NAKB: 8R7E

Classification: DNA BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2023-11-24 Released: 2024-11-27
Deposition Author(s): Thomsen, M., Thieulin-Pardo, G., Steinbacher, S., Brace, G., Tillack, K., Johnson, P., Ritzefeld, M., Schaertl, S., Frush, E., Warfield, B., Ballantyne, G., Lee, J.-H., Witte, D., Finley, M., Prasad, B., Monteagudo, E., Plotnikov, N., Pacifici, R., Maillard, M., Wilkinson, H., Iyer, R., Dominguez, C., Vogt, T., Felsenfeld, D., Haque, T.
Funding Organization(s): CHDI Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.78 Å
R-Value Free:
0.266 (Depositor), 0.265 (DCC)
R-Value Work:
0.223 (Depositor), 0.224 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Identification of orthosteric inhibitors of MutSbeta ATPase function

Brace, G., Tillack, K., Johnson, P., Ritzefeld, M., Schaertl, S., Frush, E., Warfield, B., Ballantyne, G., Lee, J.-H., Thieulin-Pardo, G., Steinbacher, S., Thomsen, M., Witte, D., Finley, M., Prasad, B., Monteagudo, E., Plotnikov, N., Pacifici, R., Maillard, M., Wilkinson, H., Iyer, R., Dominguez, C., Vogt, T., Felsenfeld, D., Haque, T.

(2024) ChemRxiv

DOI: https://doi.org/10.26434/chemrxiv-2024-74zr6

Macromolecule Content

Total Structure Weight: 449.61 kDa
Atom Count: 28,977
Modeled Residue Count: 3,456
Deposited Residue Count: 3,792
Unique protein chains: 2
Unique nucleic acid chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA mismatch repair protein Msh2	A, E	930	Homo sapiens	Mutation(s): 0 Gene Names: MSH2
UniProt & NIH Common Fund Data Resources
Find proteins for P43246 (Homo sapiens) Explore P43246 Go to UniProtKB: P43246
PHAROS: P43246 GTEx: ENSG00000095002
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P43246
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA mismatch repair protein Msh3	B, F	918	Homo sapiens	Mutation(s): 0 Gene Names: MSH3
UniProt & NIH Common Fund Data Resources
Find proteins for P20585 (Homo sapiens) Explore P20585 Go to UniProtKB: P20585
PHAROS: P20585 GTEx: ENSG00000113318
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P20585
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism
Entity ID: 3
DNA (5'-D(TPCPTPAPTPCPTPGPAPAPGPCPCPGPAPTPCPGPAPTPGPG)-3')	C, G	24	Homo sapiens
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 4
DNA (5'-D(CPAPTPCPGPAPTPCPGPCPAPGPCPTPTPCPAPGPAPTPAPGP*G)-3')	D, H	24	Homo sapiens
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
YKQ (Subject of Investigation/LOI) Query on YKQ Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain X [auth F] MOL2 format, chain L [auth B] MOL2 format, chain X [auth F] mmCIF format, chain L [auth B] mmCIF format, chain X [auth F]	L [auth B], X [auth F]	Abivertinib C₂₆ H₂₆ F N₇ O₂ UOFYSRZSLXWIQB-UHFFFAOYSA-N		Interactions Focus chain L [auth B] Focus chain X [auth F] Interactions & Density Focus chain L [auth B] Focus chain X [auth F]
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain S [auth E] MOL2 format, chain I [auth A] MOL2 format, chain S [auth E] mmCIF format, chain I [auth A] mmCIF format, chain S [auth E]	I [auth A], S [auth E]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain I [auth A] Focus chain S [auth E] Interactions & Density Focus chain I [auth A] Focus chain S [auth E]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain P [auth B] SDF format, chain Y [auth F] SDF format, chain Z [auth F] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Y [auth F] MOL2 format, chain Z [auth F] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Y [auth F] mmCIF format, chain Z [auth F]	M [auth B], N [auth B], P [auth B], Y [auth F], Z [auth F]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain M [auth B] Focus chain N [auth B] Focus chain P [auth B] Focus chain Y [auth F] Focus chain Z [auth F] Interactions & Density Focus chain M [auth B] Focus chain N [auth B] Focus chain P [auth B] Focus chain Y [auth F] Focus chain Z [auth F]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain J [auth A] SDF format, chain O [auth B] SDF format, chain R [auth B] SDF format, chain V [auth E] MOL2 format, chain AA [auth F] MOL2 format, chain J [auth A] MOL2 format, chain O [auth B] MOL2 format, chain R [auth B] MOL2 format, chain V [auth E] mmCIF format, chain AA [auth F] mmCIF format, chain J [auth A] mmCIF format, chain O [auth B] mmCIF format, chain R [auth B] mmCIF format, chain V [auth E]	AA [auth F], J [auth A], O [auth B], R [auth B], V [auth E]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth F] Focus chain J [auth A] Focus chain O [auth B] Focus chain R [auth B] Focus chain V [auth E] Interactions & Density Focus chain AA [auth F] Focus chain J [auth A] Focus chain O [auth B] Focus chain R [auth B] Focus chain V [auth E]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain Q [auth B] SDF format, chain T [auth E] SDF format, chain U [auth E] SDF format, chain W [auth E] MOL2 format, chain K [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain T [auth E] MOL2 format, chain U [auth E] MOL2 format, chain W [auth E] mmCIF format, chain K [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain T [auth E] mmCIF format, chain U [auth E] mmCIF format, chain W [auth E]	K [auth A], Q [auth B], T [auth E], U [auth E], W [auth E]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain K [auth A] Focus chain Q [auth B] Focus chain T [auth E] Focus chain U [auth E] Focus chain W [auth E] Interactions & Density Focus chain K [auth A] Focus chain Q [auth B] Focus chain T [auth E] Focus chain U [auth E] Focus chain W [auth E]