8HMQ | pdb_00008hmq

Crystal Structure of PKM2 mutant P403A

PDB DOI: https://doi.org/10.2210/pdb8HMQ/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:
0.263 (Depositor), 0.263 (DCC)
R-Value Work:
0.213 (Depositor), 0.213 (DCC)
R-Value Observed:
0.216 (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: 243.2 kDa
Atom Count: 14,873
Modeled Residue Count: 1,962
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 5 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 V [auth C] SDF format, chain O [auth B] SDF format, chain AA [auth D] MOL2 format, chain V [auth C] MOL2 format, chain O [auth B] MOL2 format, chain AA [auth D] mmCIF format, chain V [auth C] mmCIF format, chain O [auth B] mmCIF format, chain AA [auth D]	AA [auth D], O [auth B], V [auth C]	1,6-di-O-phosphono-beta-D-fructofuranose C₆ H₁₄ O₁₂ P₂ RNBGYGVWRKECFJ-ARQDHWQXSA-N		Interactions Focus chain AA [auth D] Focus chain O [auth B] Focus chain V [auth C] Interactions & Density Focus chain AA [auth D] Focus chain O [auth B] Focus chain V [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain W [auth C] SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain BA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain W [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain BA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain W [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain BA [auth D]	BA [auth D] DA [auth D] F [auth A] G [auth A] P [auth B] BA [auth D], DA [auth D], F [auth A], G [auth A], P [auth B], Q [auth B], W [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain DA [auth D] Focus chain F [auth A] Focus chain G [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain W [auth C] Interactions & Density Focus chain BA [auth D] Focus chain DA [auth D] Focus chain F [auth A] Focus chain G [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain W [auth C]
OXL Query on OXL Download:Ideal Coordinates CCD File SDF format, chain Z [auth D] SDF format, chain U [auth C] SDF format, chain N [auth B] SDF format, chain E [auth A] MOL2 format, chain Z [auth D] MOL2 format, chain U [auth C] MOL2 format, chain N [auth B] MOL2 format, chain E [auth A] mmCIF format, chain Z [auth D] mmCIF format, chain U [auth C] mmCIF format, chain N [auth B] mmCIF format, chain E [auth A]	E [auth A], N [auth B], U [auth C], Z [auth D]	OXALATE ION C₂ O₄ MUBZPKHOEPUJKR-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain N [auth B] Focus chain U [auth C] Focus chain Z [auth D] Interactions & Density Focus chain E [auth A] Focus chain N [auth B] Focus chain U [auth C] Focus chain Z [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain X [auth C] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain CA [auth D] MOL2 format, chain X [auth C] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain CA [auth D] mmCIF format, chain X [auth C] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	CA [auth D], H [auth A], I [auth A], J [auth A], X [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain X [auth C] Interactions & Density Focus chain CA [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain X [auth C]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain S [auth B] SDF format, chain Y [auth C] SDF format, chain T [auth B] SDF format, chain R [auth B] SDF format, chain M [auth A] SDF format, chain K [auth A] SDF format, chain FA [auth D] SDF format, chain EA [auth D] MOL2 format, chain L [auth A] MOL2 format, chain S [auth B] MOL2 format, chain Y [auth C] MOL2 format, chain T [auth B] MOL2 format, chain R [auth B] MOL2 format, chain M [auth A] MOL2 format, chain K [auth A] MOL2 format, chain FA [auth D] MOL2 format, chain EA [auth D] mmCIF format, chain L [auth A] mmCIF format, chain S [auth B] mmCIF format, chain Y [auth C] mmCIF format, chain T [auth B] mmCIF format, chain R [auth B] mmCIF format, chain M [auth A] mmCIF format, chain K [auth A] mmCIF format, chain FA [auth D] mmCIF format, chain EA [auth D]	EA [auth D] FA [auth D] K [auth A] L [auth A] M [auth A] EA [auth D], FA [auth D], K [auth A], L [auth A], M [auth A], R [auth B], S [auth B], T [auth B], Y [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain EA [auth D] Focus chain FA [auth D] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain Y [auth C] Interactions & Density Focus chain EA [auth D] Focus chain FA [auth D] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain Y [auth C]