1T5A

Human Pyruvate Kinase M2

PDB DOI: https://doi.org/10.2210/pdb1T5A/pdb

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

Deposited: 2004-05-03 Released: 2005-07-12
Deposition Author(s): Dombrauckas, J.D., Santarsiero, B.D., Mesecar, A.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.278
R-Value Work: 0.231

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 252.7 kDa
Atom Count: 16,271
Modelled Residue Count: 2,076
Deposited Residue Count: 2,268
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyruvate kinase, M2 isozyme	A, B, C, D	567	Homo sapiens	Mutation(s): 0 Gene Names: PKM2, PKM EC: 2.7.1.40
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
FBP Query on FBP Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain IA [auth D] SDF format, chain O [auth B] SDF format, chain X [auth C] MOL2 format, chain E [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain O [auth B] MOL2 format, chain X [auth C]	E [auth A], IA [auth D], O [auth B], 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 IA [auth D] Focus chain O [auth B] Focus chain X [auth C] Interactions & Density Focus chain E [auth A] Focus chain IA [auth D] Focus chain O [auth B] Focus chain X [auth C]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain KA [auth D] SDF format, chain Q [auth B] SDF format, chain Z [auth C] MOL2 format, chain G [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain Q [auth B] MOL2 format, chain Z [auth C]	G [auth A], KA [auth D], Q [auth B], Z [auth C]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain G [auth A] Focus chain KA [auth D] Focus chain Q [auth B] Focus chain Z [auth C] Interactions & Density Focus chain G [auth A] Focus chain KA [auth D] Focus chain Q [auth B] Focus chain Z [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain EA [auth C] SDF format, chain FA [auth C] SDF format, chain GA [auth C] SDF format, chain HA [auth C] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain NA [auth D] SDF format, chain OA [auth D] SDF format, chain PA [auth D] SDF format, chain QA [auth D] SDF format, chain RA [auth D] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth D] MOL2 format, chain OA [auth D] MOL2 format, chain PA [auth D] MOL2 format, chain QA [auth D] MOL2 format, chain RA [auth D] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B]	CA [auth C] DA [auth C] EA [auth C] FA [auth C] GA [auth C] CA [auth C], DA [auth C], EA [auth C], FA [auth C], GA [auth C], HA [auth C], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], NA [auth D], OA [auth D], PA [auth D], QA [auth D], RA [auth D], T [auth B], U [auth B], V [auth B], W [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain PA [auth D] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain PA [auth D] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B]
OXL Query on OXL Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain JA [auth D] SDF format, chain P [auth B] SDF format, chain Y [auth C] MOL2 format, chain F [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain P [auth B] MOL2 format, chain Y [auth C]	F [auth A], JA [auth D], P [auth B], Y [auth C]	OXALATE ION C₂ O₄ MUBZPKHOEPUJKR-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain JA [auth D] Focus chain P [auth B] Focus chain Y [auth C] Interactions & Density Focus chain F [auth A] Focus chain JA [auth D] Focus chain P [auth B] Focus chain Y [auth C]
K Query on K Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain I [auth A] SDF format, chain MA [auth D] SDF format, chain S [auth B] MOL2 format, chain BA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain MA [auth D] MOL2 format, chain S [auth B]	BA [auth C], I [auth A], MA [auth D], S [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Focus chain I [auth A] Focus chain MA [auth D] Focus chain S [auth B] Interactions & Density Focus chain BA [auth C] Focus chain I [auth A] Focus chain MA [auth D] Focus chain S [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain H [auth A] SDF format, chain LA [auth D] SDF format, chain R [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain H [auth A] MOL2 format, chain LA [auth D] MOL2 format, chain R [auth B]	AA [auth C], H [auth A], LA [auth D], R [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain H [auth A] Focus chain LA [auth D] Focus chain R [auth B] Interactions & Density Focus chain AA [auth C] Focus chain H [auth A] Focus chain LA [auth D] Focus chain R [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
OXL	PDBBind: 1T5A	Ki: 2.40e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.278
R-Value Work: 0.231
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.209	α = 90
b = 145.006	β = 90
c = 159.26	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
EPMR	phasing
CNS	refinement

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2005-07-12

Deposition Author(s):

Dombrauckas, J.D.

Santarsiero, B.D.

Mesecar, A.D.

Revision History (Full details and data files)

Version 1.0: 2005-07-12
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations, Structure summary
Version 1.4: 2022-12-21
Changes: Database references, Structure summary
Version 1.5: 2023-09-20
Changes: Data collection, Refinement description