6JFB | pdb_00006jfb

Crystal structure of human pyruvate kinase M2 isoform

PDB DOI: https://doi.org/10.2210/pdb6JFB/pdb

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

Deposited: 2019-02-08 Released: 2020-04-01
Deposition Author(s): Chen, T.J., Wang, W.C.
Funding Organization(s): Ministry of Science and Technology (Taiwan)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.12 Å
R-Value Free:
0.251 (Depositor), 0.269 (DCC)
R-Value Work:
0.192 (Depositor)
R-Value Observed:
0.195 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 6JFB

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of human pyruvate kinase M2 isoform

Chen, T.J., Wang, W.C.

To be published.

Macromolecule Content

Total Structure Weight: 241.98 kDa
Atom Count: 16,478
Modeled Residue Count: 2,082
Deposited Residue Count: 2,208
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyruvate kinase PKM Isoform M2	A, B, C, D	552	Homo sapiens	Mutation(s): 0 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P14618
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SER Query on SER Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain K [auth D] SDF format, chain I [auth C] SDF format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain K [auth D] MOL2 format, chain I [auth C] MOL2 format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain K [auth D] mmCIF format, chain I [auth C] mmCIF format, chain E [auth A]	E [auth A], G [auth B], I [auth C], K [auth D]	SERINE C₃ H₇ N O₃ MTCFGRXMJLQNBG-REOHCLBHSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth C] SDF format, chain H [auth B] MOL2 format, chain F [auth A] MOL2 format, chain J [auth C] MOL2 format, chain H [auth B] mmCIF format, chain F [auth A] mmCIF format, chain J [auth C] mmCIF format, chain H [auth B]	F [auth A], H [auth B], J [auth C]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.12 Å
R-Value Free: 0.251 (Depositor), 0.269 (DCC)
R-Value Work: 0.192 (Depositor)
R-Value Observed: 0.195 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.763	α = 90
b = 152.573	β = 97.88
c = 94.405	γ = 90

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2020-04-01

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Science and Technology (Taiwan)	Taiwan	--

Revision History (Full details and data files)

Version 1.0: 2020-04-01
Type: Initial release
Version 1.1: 2024-03-27
Changes: Data collection, Database references

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.