9QGT | pdb_00009qgt

Crystal Structure of human MLH1 N-terminal domain I219V with ADP-BeF3

PDB DOI: https://doi.org/10.2210/pdb9QGT/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2025-03-14 Released: 2026-10-14
Deposition Author(s): Thomsen, M., Ganichkin, O., Thieulin-Pardo, G., Bandera, A.M., Boudet, J., Finley, M., Felsenfeld, D., Haque, T., Prasad, B.C., Monteagudo, E., Vogt, T., Stamford, A.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.258 (Depositor), 0.258 (DCC)
R-Value Work:
0.218 (Depositor), 0.223 (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

Crystal Structure of human MLH1 N-terminal domain I219V with ADP-BeF3

Bandera, A.M., Thomsen, M.

To be published.

Macromolecule Content

Total Structure Weight: 155.23 kDa
Atom Count: 12,169
Modeled Residue Count: 1,339
Deposited Residue Count: 1,364
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA mismatch repair protein Mlh1	A [auth A1], B [auth B1], C [auth C1], D [auth D1]	341	Homo sapiens	Mutation(s): 1 Gene Names: MLH1, COCA2
UniProt & NIH Common Fund Data Resources
Find proteins for P40692 (Homo sapiens) Explore P40692 Go to UniProtKB: P40692
PHAROS: P40692 GTEx: ENSG00000076242
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P40692
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 10 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP (Subject of Investigation/LOI) Query on ADP Download:Ideal Coordinates CCD File SDF format, chain E [auth A1] SDF format, chain GA [auth C1] SDF format, chain PA [auth D1] SDF format, chain U [auth B1] MOL2 format, chain E [auth A1] MOL2 format, chain GA [auth C1] MOL2 format, chain PA [auth D1] MOL2 format, chain U [auth B1] mmCIF format, chain E [auth A1] mmCIF format, chain GA [auth C1] mmCIF format, chain PA [auth D1] mmCIF format, chain U [auth B1]	E [auth A1], GA [auth C1], PA [auth D1], U [auth B1]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain E [auth A1] Focus chain GA [auth C1] Focus chain PA [auth D1] Focus chain U [auth B1] Interactions & Density Focus chain E [auth A1] Focus chain GA [auth C1] Focus chain PA [auth D1] Focus chain U [auth B1]
MES Query on MES Download:Ideal Coordinates CCD File SDF format, chain K [auth A1] SDF format, chain Z [auth B1] MOL2 format, chain K [auth A1] MOL2 format, chain Z [auth B1] mmCIF format, chain K [auth A1] mmCIF format, chain Z [auth B1]	K [auth A1], Z [auth B1]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain K [auth A1] Focus chain Z [auth B1] Interactions & Density Focus chain K [auth A1] Focus chain Z [auth B1]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain MA [auth C1] SDF format, chain Q [auth A1] SDF format, chain R [auth A1] SDF format, chain VA [auth D1] SDF format, chain YA [auth D1] MOL2 format, chain MA [auth C1] MOL2 format, chain Q [auth A1] MOL2 format, chain R [auth A1] MOL2 format, chain VA [auth D1] MOL2 format, chain YA [auth D1] mmCIF format, chain MA [auth C1] mmCIF format, chain Q [auth A1] mmCIF format, chain R [auth A1] mmCIF format, chain VA [auth D1] mmCIF format, chain YA [auth D1]	MA [auth C1], Q [auth A1], R [auth A1], VA [auth D1], YA [auth D1]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain MA [auth C1] Focus chain Q [auth A1] Focus chain R [auth A1] Focus chain VA [auth D1] Focus chain YA [auth D1] Interactions & Density Focus chain MA [auth C1] Focus chain Q [auth A1] Focus chain R [auth A1] Focus chain VA [auth D1] Focus chain YA [auth D1]
BEF (Subject of Investigation/LOI) Query on BEF Download:Ideal Coordinates CCD File SDF format, chain G [auth A1] SDF format, chain IA [auth C1] SDF format, chain RA [auth D1] SDF format, chain W [auth B1] MOL2 format, chain G [auth A1] MOL2 format, chain IA [auth C1] MOL2 format, chain RA [auth D1] MOL2 format, chain W [auth B1] mmCIF format, chain G [auth A1] mmCIF format, chain IA [auth C1] mmCIF format, chain RA [auth D1] mmCIF format, chain W [auth B1]	G [auth A1], IA [auth C1], RA [auth D1], W [auth B1]	BERYLLIUM TRIFLUORIDE ION Be F₃ OGIAHMCCNXDTIE-UHFFFAOYSA-K		Interactions Focus chain G [auth A1] Focus chain IA [auth C1] Focus chain RA [auth D1] Focus chain W [auth B1] Interactions & Density Focus chain G [auth A1] Focus chain IA [auth C1] Focus chain RA [auth D1] Focus chain W [auth B1]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain CA [auth B1] SDF format, chain DA [auth B1] SDF format, chain FA [auth B1] SDF format, chain L [auth A1] SDF format, chain N [auth A1] SDF format, chain NA [auth C1] SDF format, chain OA [auth C1] SDF format, chain P [auth A1] SDF format, chain T [auth A1] SDF format, chain XA [auth D1] SDF format, chain ZA [auth D1] MOL2 format, chain CA [auth B1] MOL2 format, chain DA [auth B1] MOL2 format, chain FA [auth B1] MOL2 format, chain L [auth A1] MOL2 format, chain N [auth A1] MOL2 format, chain NA [auth C1] MOL2 format, chain OA [auth C1] MOL2 format, chain P [auth A1] MOL2 format, chain T [auth A1] MOL2 format, chain XA [auth D1] MOL2 format, chain ZA [auth D1] mmCIF format, chain CA [auth B1] mmCIF format, chain DA [auth B1] mmCIF format, chain FA [auth B1] mmCIF format, chain L [auth A1] mmCIF format, chain N [auth A1] mmCIF format, chain NA [auth C1] mmCIF format, chain OA [auth C1] mmCIF format, chain P [auth A1] mmCIF format, chain T [auth A1] mmCIF format, chain XA [auth D1] mmCIF format, chain ZA [auth D1]	CA [auth B1] DA [auth B1] FA [auth B1] L [auth A1] N [auth A1] CA [auth B1], DA [auth B1], FA [auth B1], L [auth A1], N [auth A1], NA [auth C1], OA [auth C1], P [auth A1], T [auth A1], XA [auth D1], ZA [auth D1]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain CA [auth B1] Focus chain DA [auth B1] Focus chain FA [auth B1] Focus chain L [auth A1] Focus chain N [auth A1] Focus chain NA [auth C1] Focus chain OA [auth C1] Focus chain P [auth A1] Focus chain T [auth A1] Focus chain XA [auth D1] Focus chain ZA [auth D1] Interactions & Density Focus chain CA [auth B1] Focus chain DA [auth B1] Focus chain FA [auth B1] Focus chain L [auth A1] Focus chain N [auth A1] Focus chain NA [auth C1] Focus chain OA [auth C1] Focus chain P [auth A1] Focus chain T [auth A1] Focus chain XA [auth D1] Focus chain ZA [auth D1]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain EA [auth B1] SDF format, chain LA [auth C1] SDF format, chain M [auth A1] SDF format, chain O [auth A1] SDF format, chain S [auth A1] SDF format, chain UA [auth D1] SDF format, chain WA [auth D1] MOL2 format, chain EA [auth B1] MOL2 format, chain LA [auth C1] MOL2 format, chain M [auth A1] MOL2 format, chain O [auth A1] MOL2 format, chain S [auth A1] MOL2 format, chain UA [auth D1] MOL2 format, chain WA [auth D1] mmCIF format, chain EA [auth B1] mmCIF format, chain LA [auth C1] mmCIF format, chain M [auth A1] mmCIF format, chain O [auth A1] mmCIF format, chain S [auth A1] mmCIF format, chain UA [auth D1] mmCIF format, chain WA [auth D1]	EA [auth B1] LA [auth C1] M [auth A1] O [auth A1] S [auth A1] EA [auth B1], LA [auth C1], M [auth A1], O [auth A1], S [auth A1], UA [auth D1], WA [auth D1]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain EA [auth B1] Focus chain LA [auth C1] Focus chain M [auth A1] Focus chain O [auth A1] Focus chain S [auth A1] Focus chain UA [auth D1] Focus chain WA [auth D1] Interactions & Density Focus chain EA [auth B1] Focus chain LA [auth C1] Focus chain M [auth A1] Focus chain O [auth A1] Focus chain S [auth A1] Focus chain UA [auth D1] Focus chain WA [auth D1]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain I [auth A1] SDF format, chain J [auth A1] SDF format, chain KA [auth C1] SDF format, chain TA [auth D1] SDF format, chain Y [auth B1] MOL2 format, chain I [auth A1] MOL2 format, chain J [auth A1] MOL2 format, chain KA [auth C1] MOL2 format, chain TA [auth D1] MOL2 format, chain Y [auth B1] mmCIF format, chain I [auth A1] mmCIF format, chain J [auth A1] mmCIF format, chain KA [auth C1] mmCIF format, chain TA [auth D1] mmCIF format, chain Y [auth B1]	I [auth A1], J [auth A1], KA [auth C1], TA [auth D1], Y [auth B1]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain I [auth A1] Focus chain J [auth A1] Focus chain KA [auth C1] Focus chain TA [auth D1] Focus chain Y [auth B1] Interactions & Density Focus chain I [auth A1] Focus chain J [auth A1] Focus chain KA [auth C1] Focus chain TA [auth D1] Focus chain Y [auth B1]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain AA [auth B1] SDF format, chain BA [auth B1] MOL2 format, chain AA [auth B1] MOL2 format, chain BA [auth B1] mmCIF format, chain AA [auth B1] mmCIF format, chain BA [auth B1]	AA [auth B1], BA [auth B1]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth B1] Focus chain BA [auth B1] Interactions & Density Focus chain AA [auth B1] Focus chain BA [auth B1]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain F [auth A1] SDF format, chain HA [auth C1] SDF format, chain QA [auth D1] SDF format, chain V [auth B1] MOL2 format, chain F [auth A1] MOL2 format, chain HA [auth C1] MOL2 format, chain QA [auth D1] MOL2 format, chain V [auth B1] mmCIF format, chain F [auth A1] mmCIF format, chain HA [auth C1] mmCIF format, chain QA [auth D1] mmCIF format, chain V [auth B1]	F [auth A1], HA [auth C1], QA [auth D1], V [auth B1]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A1] Focus chain HA [auth C1] Focus chain QA [auth D1] Focus chain V [auth B1] Interactions & Density Focus chain F [auth A1] Focus chain HA [auth C1] Focus chain QA [auth D1] Focus chain V [auth B1]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain H [auth A1] SDF format, chain JA [auth C1] SDF format, chain SA [auth D1] SDF format, chain X [auth B1] MOL2 format, chain H [auth A1] MOL2 format, chain JA [auth C1] MOL2 format, chain SA [auth D1] MOL2 format, chain X [auth B1] mmCIF format, chain H [auth A1] mmCIF format, chain JA [auth C1] mmCIF format, chain SA [auth D1] mmCIF format, chain X [auth B1]	H [auth A1], JA [auth C1], SA [auth D1], X [auth B1]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain H [auth A1] Focus chain JA [auth C1] Focus chain SA [auth D1] Focus chain X [auth B1] Interactions & Density Focus chain H [auth A1] Focus chain JA [auth C1] Focus chain SA [auth D1] Focus chain X [auth B1]