9QIL | pdb_00009qil

Crystal Structure of human PMS1 N-terminal domain N309S with ADP

PDB DOI: https://doi.org/10.2210/pdb9QIL/pdb

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

Deposited: 2025-03-17 Released: 2026-09-30
Deposition Author(s): Bandera, A.M., Thomsen, M.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.86 Å
R-Value Free:
0.243 (Depositor), 0.246 (DCC)
R-Value Work:
0.211 (Depositor), 0.217 (DCC)

Starting Model: in silico
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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 PMS1 N-terminal domain N309S with ATPgammaS

Bandera, A.M., Thomsen, M.

To be published.

Macromolecule Content

Total Structure Weight: 156.1 kDa
Atom Count: 11,868
Modeled Residue Count: 1,366
Deposited Residue Count: 1,368
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PMS1 protein homolog 1	A, B, C, D	342	Homo sapiens	Mutation(s): 1 Gene Names: PMS1, PMSL1
UniProt & NIH Common Fund Data Resources
Find proteins for P54277 (Homo sapiens) Explore P54277 Go to UniProtKB: P54277
PHAROS: P54277 GTEx: ENSG00000064933
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P54277
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 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 AA [auth D] SDF format, chain E [auth A] SDF format, chain M [auth B] SDF format, chain T [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain E [auth A] MOL2 format, chain M [auth B] MOL2 format, chain T [auth C] mmCIF format, chain AA [auth D] mmCIF format, chain E [auth A] mmCIF format, chain M [auth B] mmCIF format, chain T [auth C]	AA [auth D], E [auth A], M [auth B], T [auth C]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain AA [auth D] Focus chain E [auth A] Focus chain M [auth B] Focus chain T [auth C] Interactions & Density Focus chain AA [auth D] Focus chain E [auth A] Focus chain M [auth B] Focus chain T [auth C]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth A] MOL2 format, chain G [auth A] MOL2 format, chain J [auth A] mmCIF format, chain G [auth A] mmCIF format, chain J [auth A]	G [auth A], J [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain J [auth A] Interactions & Density Focus chain G [auth A] Focus chain J [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain EA [auth D] SDF format, chain I [auth A] SDF format, chain L [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain V [auth C] SDF format, chain X [auth C] MOL2 format, chain CA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain L [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain V [auth C] MOL2 format, chain X [auth C] mmCIF format, chain CA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain L [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain V [auth C] mmCIF format, chain X [auth C]	CA [auth D] EA [auth D] I [auth A] L [auth A] O [auth B] CA [auth D], EA [auth D], I [auth A], L [auth A], O [auth B], P [auth B], V [auth C], X [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Focus chain EA [auth D] Focus chain I [auth A] Focus chain L [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain V [auth C] Focus chain X [auth C] Interactions & Density Focus chain CA [auth D] Focus chain EA [auth D] Focus chain I [auth A] Focus chain L [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain V [auth C] Focus chain X [auth C]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain H [auth A] SDF format, chain K [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain W [auth C] SDF format, chain Y [auth C] SDF format, chain Z [auth C] MOL2 format, chain DA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain K [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain W [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] mmCIF format, chain DA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain K [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain W [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C]	DA [auth D] H [auth A] K [auth A] Q [auth B] R [auth B] DA [auth D], H [auth A], K [auth A], Q [auth B], R [auth B], S [auth B], W [auth C], Y [auth C], Z [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain DA [auth D] Focus chain H [auth A] Focus chain K [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain W [auth C] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain DA [auth D] Focus chain H [auth A] Focus chain K [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain W [auth C] Focus chain Y [auth C] Focus chain Z [auth C]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain F [auth A] SDF format, chain N [auth B] SDF format, chain U [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain N [auth B] MOL2 format, chain U [auth C] mmCIF format, chain BA [auth D] mmCIF format, chain F [auth A] mmCIF format, chain N [auth B] mmCIF format, chain U [auth C]	BA [auth D], F [auth A], N [auth B], U [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain F [auth A] Focus chain N [auth B] Focus chain U [auth C] Interactions & Density Focus chain BA [auth D] Focus chain F [auth A] Focus chain N [auth B] Focus chain U [auth C]