8XFD | pdb_00008xfd

Crystal structure of pyruvate kinase tetramer in complex with allosteric activator, Mitapivat (MTPV, AG-348)

PDB DOI: https://doi.org/10.2210/pdb8XFD/pdb

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

Deposited: 2023-12-13 Released: 2024-05-15
Deposition Author(s): Sun, R., Achour, A.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.265 (Depositor), 0.260 (DCC)
R-Value Work:
0.232 (Depositor), 0.230 (DCC)
R-Value Observed:
0.233 (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

High Resolution Crystal Structure of the Pyruvate Kinase Tetramer in Complex with the Allosteric Activator Mitapivat/AG-348

Han, X., Sandalova, T., Zhang, C., Mardinoglu, A., Achour, A., Sun, R.

(2024) Crystals (Basel)

DOI: https://doi.org/10.3390/cryst14050441

Macromolecule Content

Total Structure Weight: 236.62 kDa
Atom Count: 16,621
Modeled Residue Count: 2,059
Deposited Residue Count: 2,172
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform L-type of Pyruvate kinase PKLR	A, B, C, D	543	Homo sapiens	Mutation(s): 0 Gene Names: PKLR, PK1, PKL EC: 2.7.1.40
UniProt & NIH Common Fund Data Resources
Find proteins for P30613 (Homo sapiens) Explore P30613 Go to UniProtKB: P30613
PHAROS: P30613 GTEx: ENSG00000143627
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P30613
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
WV2 Query on WV2 Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain N [auth D] MOL2 format, chain I [auth B] MOL2 format, chain N [auth D] mmCIF format, chain I [auth B] mmCIF format, chain N [auth D]	I [auth B], N [auth D]	mitapivat C₂₄ H₂₆ N₄ O₃ S XAYGBKHKBBXDAK-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain N [auth D] Interactions & Density Focus chain I [auth B] Focus chain N [auth D]
FBP Query on FBP Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain K [auth C] SDF format, chain M [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain K [auth C] MOL2 format, chain M [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain K [auth C] mmCIF format, chain M [auth D]	F [auth A], H [auth B], K [auth C], M [auth D]	1,6-di-O-phosphono-beta-D-fructofuranose C₆ H₁₄ O₁₂ P₂ RNBGYGVWRKECFJ-ARQDHWQXSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain M [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain M [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D]	E [auth A], G [auth B], J [auth C], L [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain J [auth C] Focus chain L [auth D]