4YJ5 | pdb_00004yj5

Crystal structure of PKM2 mutant

PDB DOI: https://doi.org/10.2210/pdb4YJ5/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2015-03-03 Released: 2016-03-09
Deposition Author(s): Liu, J.-S., Wu, C.-W., Wang, W.-C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.41 Å
R-Value Free:
0.217 (Depositor), 0.220 (DCC)
R-Value Work:
0.144 (Depositor), 0.160 (DCC)
R-Value Observed:
0.148 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Literature

Mutations in the PKM2 exon-10 region are associated with reduced allostery and increased nuclear translocation

Chen, T.J., Wang, H.J., Liu, J.S., Cheng, H.H., Hsu, S.C., Wu, M.C., Lu, C.H., Wu, Y.F., Wu, J.W., Liu, Y.Y., Kung, H.J., Wang, W.C.

(2019) Commun Biol 2

DOI: https://doi.org/10.1038/s42003-019-0343-4

Macromolecule Content

Total Structure Weight: 228.62 kDa
Atom Count: 16,419
Modelled Residue Count: 2,072
Deposited Residue Count: 2,072
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 PKM	A, B, C, D	518	Homo sapiens	Mutation(s): 1 Gene Names: PKM, OIP3, PK2, PK3, PKM2 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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FBP Query on FBP Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain O [auth C] SDF format, chain S [auth D] MOL2 format, chain K [auth B] MOL2 format, chain O [auth C] MOL2 format, chain S [auth D] mmCIF format, chain K [auth B] mmCIF format, chain O [auth C] mmCIF format, chain S [auth D]	K [auth B], O [auth C], S [auth D]	1,6-di-O-phosphono-beta-D-fructofuranose C₆ H₁₄ O₁₂ P₂ RNBGYGVWRKECFJ-ARQDHWQXSA-N		Interactions Focus chain K [auth B] Focus chain O [auth C] Focus chain S [auth D] Interactions & Density Focus chain K [auth B] Focus chain O [auth C] Focus chain S [auth D]
SER Query on SER Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain N [auth C] SDF format, chain R [auth D] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain N [auth C] MOL2 format, chain R [auth D] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain N [auth C] mmCIF format, chain R [auth D]	G [auth A], J [auth B], N [auth C], R [auth D]	SERINE C₃ H₇ N O₃ MTCFGRXMJLQNBG-REOHCLBHSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain R [auth D] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain R [auth D]
PYR Query on PYR Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain L [auth C] SDF format, chain P [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain L [auth C] MOL2 format, chain P [auth D] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain L [auth C] mmCIF format, chain P [auth D]	E [auth A], H [auth B], L [auth C], P [auth D]	PYRUVIC ACID C₃ H₄ O₃ LCTONWCANYUPML-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain L [auth C] Focus chain P [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain L [auth C] Focus chain P [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain M [auth C] SDF format, chain Q [auth D] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain M [auth C] MOL2 format, chain Q [auth D] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain M [auth C] mmCIF format, chain Q [auth D]	F [auth A], I [auth B], M [auth C], Q [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain Q [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain Q [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.41 Å
R-Value Free: 0.217 (Depositor), 0.220 (DCC)
R-Value Work: 0.144 (Depositor), 0.160 (DCC)
R-Value Observed: 0.148 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.217	α = 90
b = 140.887	β = 93.97
c = 108.72	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
AMoRE	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2016-03-09

Deposition Author(s):

Liu, J.-S.

Wu, C.-W.

Wang, W.-C.

Funding Organization	Location	Grant Number
	Taiwan	--

Revision History (Full details and data files)

Version 1.0: 2016-03-09
Type: Initial release
Version 1.1: 2019-04-03
Changes: Data collection, Database references, Derived calculations
Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.3: 2023-11-08
Changes: Data collection, Database references, Refinement description, Structure summary
Version 2.0: 2023-11-15
Changes: Atomic model, Data collection