8HMU | pdb_00008hmu

Crystal Structure of PKM2 mutant R516C

PDB DOI: https://doi.org/10.2210/pdb8HMU/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2022-12-05 Released: 2023-01-11
Deposition Author(s): Upadhyay, S., Kumar, A., Patel, A.K.
Funding Organization(s): Department of Biotechnology (DBT, India)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.279 (Depositor), 0.279 (DCC)
R-Value Work:
0.237 (Depositor), 0.237 (DCC)
R-Value Observed:
0.239 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structural and mechanistic insights into cancer patient-derived mutations in Pyruvate Kinase muscle isoform 2

Upadhyay, S., Kumar, A., Patel, A.K.

To be published.

Macromolecule Content

Total Structure Weight: 244.42 kDa
Atom Count: 15,451
Modeled Residue Count: 2,008
Deposited Residue Count: 2,204
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyruvate kinase PKM	A, B, C, D	551	Homo sapiens	Mutation(s): 1 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P14618
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FBP (Subject of Investigation/LOI) Query on FBP Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain EA [auth D] SDF format, chain M [auth B] SDF format, chain V [auth C] SDF format, chain X [auth C] MOL2 format, chain E [auth A] MOL2 format, chain EA [auth D] MOL2 format, chain M [auth B] MOL2 format, chain V [auth C] MOL2 format, chain X [auth C] mmCIF format, chain E [auth A] mmCIF format, chain EA [auth D] mmCIF format, chain M [auth B] mmCIF format, chain V [auth C] mmCIF format, chain X [auth C]	E [auth A], EA [auth D], M [auth B], V [auth C], X [auth C]	1,6-di-O-phosphono-beta-D-fructofuranose C₆ H₁₄ O₁₂ P₂ RNBGYGVWRKECFJ-ARQDHWQXSA-N		Interactions Focus chain E [auth A] Focus chain EA [auth D] Focus chain M [auth B] Focus chain V [auth C] Focus chain X [auth C] Interactions & Density Focus chain E [auth A] Focus chain EA [auth D] Focus chain M [auth B] Focus chain V [auth C] Focus chain X [auth C]
PO4 (Subject of Investigation/LOI) Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth C] SDF format, chain GA [auth D] SDF format, chain H [auth A] SDF format, chain HA [auth D] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain KA [auth D] SDF format, chain LA [auth D] SDF format, chain T [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain GA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain LA [auth D] MOL2 format, chain T [auth B] mmCIF format, chain AA [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain GA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain KA [auth D] mmCIF format, chain LA [auth D] mmCIF format, chain T [auth B]	AA [auth C] BA [auth C] GA [auth D] H [auth A] HA [auth D] AA [auth C], BA [auth C], GA [auth D], H [auth A], HA [auth D], I [auth A], J [auth A], KA [auth D], LA [auth D], T [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain GA [auth D] Focus chain H [auth A] Focus chain HA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain KA [auth D] Focus chain LA [auth D] Focus chain T [auth B] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain GA [auth D] Focus chain H [auth A] Focus chain HA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain KA [auth D] Focus chain LA [auth D] Focus chain T [auth B]
GOL (Subject of Investigation/LOI) Query on GOL Download:Ideal Coordinates CCD File SDF format, chain JA [auth D] SDF format, chain Q [auth B] MOL2 format, chain JA [auth D] MOL2 format, chain Q [auth B] mmCIF format, chain JA [auth D] mmCIF format, chain Q [auth B]	JA [auth D], Q [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain JA [auth D] Focus chain Q [auth B] Interactions & Density Focus chain JA [auth D] Focus chain Q [auth B]
OXL (Subject of Investigation/LOI) Query on OXL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain FA [auth D] SDF format, chain N [auth B] SDF format, chain R [auth B] SDF format, chain W [auth C] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth D] MOL2 format, chain N [auth B] MOL2 format, chain R [auth B] MOL2 format, chain W [auth C] mmCIF format, chain F [auth A] mmCIF format, chain FA [auth D] mmCIF format, chain N [auth B] mmCIF format, chain R [auth B] mmCIF format, chain W [auth C]	F [auth A], FA [auth D], N [auth B], R [auth B], W [auth C]	OXALATE ION C₂ O₄ MUBZPKHOEPUJKR-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain FA [auth D] Focus chain N [auth B] Focus chain R [auth B] Focus chain W [auth C] Interactions & Density Focus chain F [auth A] Focus chain FA [auth D] Focus chain N [auth B] Focus chain R [auth B] Focus chain W [auth C]
EDO (Subject of Investigation/LOI) Query on EDO Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain IA [auth D] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain S [auth B] SDF format, chain Y [auth C] SDF format, chain Z [auth C] MOL2 format, chain G [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain S [auth B] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] mmCIF format, chain G [auth A] mmCIF format, chain IA [auth D] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain S [auth B] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C]	G [auth A] IA [auth D] O [auth B] P [auth B] S [auth B] G [auth A], IA [auth D], O [auth B], P [auth B], S [auth B], Y [auth C], Z [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain IA [auth D] Focus chain O [auth B] Focus chain P [auth B] Focus chain S [auth B] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain G [auth A] Focus chain IA [auth D] Focus chain O [auth B] Focus chain P [auth B] Focus chain S [auth B] Focus chain Y [auth C] Focus chain Z [auth C]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain MA [auth D] SDF format, chain NA [auth D] SDF format, chain U [auth B] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain MA [auth D] MOL2 format, chain NA [auth D] MOL2 format, chain U [auth B] mmCIF format, chain CA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain MA [auth D] mmCIF format, chain NA [auth D] mmCIF format, chain U [auth B]	CA [auth C] DA [auth C] K [auth A] L [auth A] MA [auth D] CA [auth C], DA [auth C], K [auth A], L [auth A], MA [auth D], NA [auth D], U [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain CA [auth C] Focus chain DA [auth C] Focus chain K [auth A] Focus chain L [auth A] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain U [auth B] Interactions & Density Focus chain CA [auth C] Focus chain DA [auth C] Focus chain K [auth A] Focus chain L [auth A] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain U [auth B]