3U2Z

Activator-Bound Structure of Human Pyruvate Kinase M2

PDB DOI: https://doi.org/10.2210/pdb3U2Z/pdb

Classification: transferase/transferase activator
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-10-04 Released: 2012-09-12
Deposition Author(s): Hong, B., Dimov, S., Tempel, W., Auld, D., Thomas, C., Boxer, M., Jianq, J.-K., Skoumbourdis, A., Min, S., Southall, N., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Inglese, J., Park, H., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.231
R-Value Work: 0.190
R-Value Observed: 0.191

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 234.75 kDa
Atom Count: 15,896
Modelled Residue Count: 2,063
Deposited Residue Count: 2,132
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 isozymes M1/M2	A, B, C, D	533	Homo sapiens	Mutation(s): 0 Gene Names: PKM2, OIP3, PK2, PK3, 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
07T Query on 07T Download Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain T [auth C] MOL2 format, chain L [auth B] MOL2 format, chain T [auth C]	L [auth B], T [auth C]	6-(3-aminobenzyl)-4-methyl-2-methylsulfinyl-4,6-dihydro-5H-thieno[2',3':4,5]pyrrolo[2,3-d]pyridazin-5-one C₁₇ H₁₆ N₄ O₂ S₂ ZWKJWVSEDISQIS-RUZDIDTESA-N		Interactions Focus chain L [auth B] Focus chain T [auth C] Interactions & Density Focus chain L [auth B] Focus chain T [auth C]
FBP Query on FBP Download Ideal Coordinates CCD File SDF format, chain S [auth C] SDF format, chain Y [auth D] SDF format, chain E [auth A] SDF format, chain M [auth B] MOL2 format, chain S [auth C] MOL2 format, chain Y [auth D] MOL2 format, chain E [auth A] MOL2 format, chain M [auth B]	E [auth A], M [auth B], S [auth C], Y [auth D]	1,6-di-O-phosphono-beta-D-fructofuranose C₆ H₁₄ O₁₂ P₂ RNBGYGVWRKECFJ-ARQDHWQXSA-N		Interactions Focus chain E [auth A] Focus chain M [auth B] Focus chain S [auth C] Focus chain Y [auth D] Interactions & Density Focus chain E [auth A] Focus chain M [auth B] Focus chain S [auth C] Focus chain Y [auth D]
UNX Query on UNX Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain H [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain R [auth B] SDF format, chain AA [auth D] SDF format, chain DA [auth D] SDF format, chain EA [auth D] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain Q [auth B] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain Z [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain R [auth B] MOL2 format, chain AA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain Z [auth D]	AA [auth D] BA [auth D] CA [auth D] DA [auth D] EA [auth D] AA [auth D], BA [auth D], CA [auth D], DA [auth D], EA [auth D], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], U [auth C], V [auth C], W [auth C], X [auth C], Z [auth D]	UNKNOWN ATOM OR ION X		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Z [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.231
R-Value Work: 0.190
R-Value Observed: 0.191
Space Group: P 1 2₁ 1
Diffraction Data: https://doi.org/10.18430/m33u2z

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.762	α = 90
b = 151.163	β = 102.94
c = 93.213	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-09-12

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2012-09-12
Type: Initial release
Version 1.1: 2013-01-02
Changes: Database references
Version 1.2: 2017-11-08
Changes: Refinement description
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations, Structure summary
Version 1.4: 2023-09-13
Changes: Data collection, Database references, Refinement description, Structure summary