3GQY | pdb_00003gqy

Activator-Bound Structure of Human Pyruvate Kinase M2

PDB DOI: https://doi.org/10.2210/pdb3GQY/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: 1.85 Å
R-Value Free:
0.238 (Depositor), 0.236 (DCC)
R-Value Work:
0.213 (Depositor), 0.213 (DCC)
R-Value Observed:
0.213 (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: 243.37 kDa
Atom Count: 15,931
Modeled Residue Count: 2,038
Deposited Residue Count: 2,200
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P14618
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DZG Query on DZG Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain O [auth C] MOL2 format, chain H [auth B] MOL2 format, chain O [auth C] mmCIF format, chain H [auth B] mmCIF format, chain O [auth C]	H [auth B], O [auth C]	1-(2,3-dihydro-1,4-benzodioxin-6-ylsulfonyl)-4-[(4-methoxyphenyl)sulfonyl]piperazine C₁₉ H₂₂ N₂ O₇ S₂ HMGDKYUJSFVHIY-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Focus chain O [auth C] Interactions & Density Focus chain H [auth B] Focus chain O [auth C]
FBP Query on FBP Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] SDF format, chain P [auth C] SDF format, chain T [auth D] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain P [auth C] MOL2 format, chain T [auth D] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain P [auth C] mmCIF format, chain T [auth D]	E [auth A], I [auth B], P [auth C], T [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 I [auth B] Focus chain P [auth C] Focus chain T [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain P [auth C] Focus chain T [auth D]
TLA Query on TLA Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain Q [auth C] SDF format, chain U [auth D] SDF format, chain V [auth D] SDF format, chain K [auth B] SDF format, chain J [auth B] MOL2 format, chain F [auth A] MOL2 format, chain Q [auth C] MOL2 format, chain U [auth D] MOL2 format, chain V [auth D] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] mmCIF format, chain F [auth A] mmCIF format, chain Q [auth C] mmCIF format, chain U [auth D] mmCIF format, chain V [auth D] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B]	F [auth A] J [auth B] K [auth B] Q [auth C] U [auth D] F [auth A], J [auth B], K [auth B], Q [auth C], U [auth D], V [auth D]	L(+)-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-JCYAYHJZSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain Q [auth C] Focus chain U [auth D] Focus chain V [auth D] Interactions & Density Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain Q [auth C] Focus chain U [auth D] Focus chain V [auth D]
UNX Query on UNX Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth B] SDF format, chain N [auth B] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain W [auth D] SDF format, chain X [auth D] SDF format, chain Y [auth D] SDF format, chain M [auth B] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain N [auth B] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain M [auth B] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain N [auth B] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain W [auth D] mmCIF format, chain X [auth D] mmCIF format, chain Y [auth D] mmCIF format, chain M [auth B]	G [auth A] L [auth B] M [auth B] N [auth B] R [auth C] G [auth A], L [auth B], M [auth B], N [auth B], R [auth C], S [auth C], W [auth D], X [auth D], Y [auth D]	UNKNOWN ATOM OR ION X		Interactions Focus chain G [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Interactions & Density Focus chain G [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.238 (Depositor), 0.236 (DCC)
R-Value Work: 0.213 (Depositor), 0.213 (DCC)
R-Value Observed: 0.213 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.149	α = 90
b = 152.952	β = 103.28
c = 93.159	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
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

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