9HIB | pdb_00009hib

K115 acetylated human muscle pyruvate kinase, isoform M2 (PKM2)

PDB DOI: https://doi.org/10.2210/pdb9HIB/pdb

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

Deposited: 2024-11-25 Released: 2025-11-05
Deposition Author(s): Pavlenko, D., Nudelman, H., Shahar, A., Arbely, E.
Funding Organization(s): European Research Council (ERC), Israel Science Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.17 Å
R-Value Free:
0.265 (Depositor), 0.267 (DCC)
R-Value Work:
0.223 (Depositor), 0.226 (DCC)
R-Value Observed:
0.225 (Depositor)

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

Isoform-specific regulation of PKM by acetylation

Pavlenko, D., Tamargo-Azpilicueta, J., Ankri, Y., Nudelman, H., Shahar, A., Diez-Moreno, I., Arbely, E.

(2025) Proc Natl Acad Sci U S A

Macromolecule Content

Total Structure Weight: 236.96 kDa
Atom Count: 16,021
Modeled Residue Count: 2,037
Deposited Residue Count: 2,148
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyruvate kinase PKM	A, B, C, D	537	Homo sapiens	Mutation(s): 0 Gene Names: PKM, OIP3, PK2, PK3, PKM2 EC: 2.7.1.40 (PDB Primary Data), 2.7.11.1 (PDB Primary Data), 2.7.10.2 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P14618 (Homo sapiens) Explore P14618 Go to UniProtKB: P14618
PHAROS: P14618 GTEx: ENSG00000067225
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P14618
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TRS (Subject of Investigation/LOI) Query on TRS Download Ideal Coordinates CCD File SDF format, chain N [auth C] MOL2 format, chain N [auth C] mmCIF format, chain N [auth C]	N [auth C]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain N [auth C] Interactions & Density Focus chain N [auth C]
SIN (Subject of Investigation/LOI) Query on SIN Download Ideal Coordinates CCD File SDF format, chain Q [auth C] MOL2 format, chain Q [auth C] mmCIF format, chain Q [auth C]	Q [auth C]	SUCCINIC ACID C₄ H₆ O₄ KDYFGRWQOYBRFD-UHFFFAOYSA-N		Interactions Focus chain Q [auth C] Interactions & Density Focus chain Q [auth C]
GOL (Subject of Investigation/LOI) Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain M [auth C] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain V [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain M [auth C] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain V [auth D] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain M [auth C] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain V [auth D]	E [auth A] H [auth B] M [auth C] R [auth C] S [auth C] E [auth A], H [auth B], M [auth C], R [auth C], S [auth C], V [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain M [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain V [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain M [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain V [auth D]
EDO (Subject of Investigation/LOI) Query on EDO Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain L [auth C] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain T [auth C] SDF format, chain W [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain L [auth C] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain T [auth C] MOL2 format, chain W [auth D] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain L [auth C] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C] mmCIF format, chain T [auth C] mmCIF format, chain W [auth D]	F [auth A] G [auth A] I [auth B] J [auth B] L [auth C] F [auth A], G [auth A], I [auth B], J [auth B], L [auth C], O [auth C], P [auth C], T [auth C], W [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain T [auth C] Focus chain W [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain T [auth C] Focus chain W [auth D]
K (Subject of Investigation/LOI) Query on K Download Ideal Coordinates CCD File SDF format, chain U [auth C] MOL2 format, chain U [auth C] mmCIF format, chain U [auth C]	U [auth C]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain U [auth C] Interactions & Density Focus chain U [auth C]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain K [auth B] MOL2 format, chain K [auth B] mmCIF format, chain K [auth B]	K [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Interactions & Density Focus chain K [auth B]