3GR4

Activator-Bound Structure of Human Pyruvate Kinase M2

PDB DOI: https://doi.org/10.2210/pdb3GR4/pdb

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

Deposited: 2009-03-24 Released: 2009-04-07
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., Bochkarev, A., Inglese, J., Park, H., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.231 (Depositor), 0.230 (DCC)
R-Value Work:
0.208 (Depositor), 0.210 (DCC)
R-Value Observed:
0.208 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Activator-Bound Structures of Human Pyruvate Kinase M2

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., Bochkarev, A., Inglese, J., Park, H.

To be published.

Macromolecule Content

Total Structure Weight: 243.96 kDa
Atom Count: 16,503
Modelled Residue Count: 2,048
Deposited Residue Count: 2,200
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	550	Homo sapiens	Mutation(s): 0 Gene Names: PKM2, PK2, PK3, PKM EC: 2.7.1.40 (PDB Primary Data), 2.7.11.1 (UniProt), 2.7.10.2 (UniProt)
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 LOADING

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DYY Query on DYY Download Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain G [auth A] MOL2 format, chain CA [auth D] MOL2 format, chain G [auth A] mmCIF format, chain CA [auth D] mmCIF format, chain G [auth A]	CA [auth D], G [auth A]	1-[(2,6-difluorophenyl)sulfonyl]-4-(2,3-dihydro-1,4-benzodioxin-6-ylsulfonyl)piperazine C₁₈ H₁₈ F₂ N₂ O₆ S₂ SHWNKRPMUBFWKE-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Focus chain G [auth A] Interactions & Density Focus chain CA [auth D] Focus chain G [auth A]
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain N [auth A] MOL2 format, chain N [auth A] mmCIF format, chain N [auth A]	N [auth A]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain N [auth A] Interactions & Density Focus chain N [auth A]
FBP Query on FBP Download Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain E [auth A] SDF format, chain O [auth B] SDF format, chain X [auth C] MOL2 format, chain DA [auth D] MOL2 format, chain E [auth A] MOL2 format, chain O [auth B] MOL2 format, chain X [auth C] mmCIF format, chain DA [auth D] mmCIF format, chain E [auth A] mmCIF format, chain O [auth B] mmCIF format, chain X [auth C]	DA [auth D], E [auth A], O [auth B], X [auth C]	1,6-di-O-phosphono-beta-D-fructofuranose C₆ H₁₄ O₁₂ P₂ RNBGYGVWRKECFJ-ARQDHWQXSA-N		Interactions Focus chain DA [auth D] Focus chain E [auth A] Focus chain O [auth B] Focus chain X [auth C] Interactions & Density Focus chain DA [auth D] Focus chain E [auth A] Focus chain O [auth B] Focus chain X [auth C]
TLA Query on TLA Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain EA [auth D] SDF format, chain F [auth A] SDF format, chain JA [auth D] SDF format, chain P [auth B] SDF format, chain W [auth B] SDF format, chain Y [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain EA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain P [auth B] MOL2 format, chain W [auth B] MOL2 format, chain Y [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain EA [auth D] mmCIF format, chain F [auth A] mmCIF format, chain JA [auth D] mmCIF format, chain P [auth B] mmCIF format, chain W [auth B] mmCIF format, chain Y [auth C]	BA [auth C] EA [auth D] F [auth A] JA [auth D] P [auth B] BA [auth C], EA [auth D], F [auth A], JA [auth D], P [auth B], W [auth B], Y [auth C]	L(+)-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-JCYAYHJZSA-N		Interactions Focus chain BA [auth C] Focus chain EA [auth D] Focus chain F [auth A] Focus chain JA [auth D] Focus chain P [auth B] Focus chain W [auth B] Focus chain Y [auth C] Interactions & Density Focus chain BA [auth C] Focus chain EA [auth D] Focus chain F [auth A] Focus chain JA [auth D] Focus chain P [auth B] Focus chain W [auth B] Focus chain Y [auth C]
UNX Query on UNX Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain FA [auth D] 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 IA [auth D] 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 Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain Z [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain FA [auth D] 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 IA [auth D] 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 Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain Z [auth C] mmCIF format, chain AA [auth C] mmCIF format, chain FA [auth D] 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 IA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain Z [auth C]	AA [auth C] FA [auth D] GA [auth D] H [auth A] HA [auth D] AA [auth C], FA [auth D], GA [auth D], H [auth A], HA [auth D], I [auth A], IA [auth D], J [auth A], K [auth A], L [auth A], M [auth A], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], Z [auth C]	UNKNOWN ATOM OR ION X		Interactions Focus chain AA [auth C] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain H [auth A] Focus chain HA [auth D] Focus chain I [auth A] Focus chain IA [auth D] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain H [auth A] Focus chain HA [auth D] Focus chain I [auth A] Focus chain IA [auth D] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain Z [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.231 (Depositor), 0.230 (DCC)
R-Value Work: 0.208 (Depositor), 0.210 (DCC)
R-Value Observed: 0.208 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.275	α = 90
b = 153.206	β = 102.91
c = 93.138	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
Coot	model building
MolProbity	model building
prodrg	refinement

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2009-04-07

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2009-04-07
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-01
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: 2023-09-06
Changes: Data collection, Database references, Refinement description, Structure summary