3SRH | pdb_00003srh

Human M2 pyruvate kinase

PDB DOI: https://doi.org/10.2210/pdb3SRH/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-07-07 Released: 2012-08-08
Deposition Author(s): Morgan, H.P., O'Reilly, F., Palmer, R., McNae, I.W., Nowicki, M.W., Wear, M.A., Fothergill-Gilmore, L.A., Walkinshaw, M.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.270 (Depositor), 0.268 (DCC)
R-Value Work:
0.217 (Depositor), 0.216 (DCC)
R-Value Observed:
0.219 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3SRH

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

Literature

Allosetric regulation of M2 pyruvate kinase.

Morgan, H.P., O'Reilly, F., Palmer, R., McNae, I.W., Nowicki, M.W., Wear, M.A., Fothergill-Gilmore, L.A., Walkinshaw, M.D.

To be published.

Macromolecule Content

Total Structure Weight: 241.04 kDa
Atom Count: 16,232
Modeled Residue Count: 2,072
Deposited Residue Count: 2,204
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyruvate kinase isozymes M1/M2	A, B, C, D	551	Homo sapiens	Mutation(s): 0 Gene Names: OIP3, PK2, PK3, PKM, 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain G [auth D] SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain G [auth D] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain G [auth D] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	E [auth A], F [auth B], G [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.270 (Depositor), 0.268 (DCC)
R-Value Work: 0.217 (Depositor), 0.216 (DCC)
R-Value Observed: 0.219 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.2	α = 90
b = 154.31	β = 105.59
c = 98.59	γ = 90

Software Package:

Software Name	Purpose
DNA	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2012-08-08

Deposition Author(s):

Fothergill-Gilmore, L.A.

Walkinshaw, M.D.

Revision History (Full details and data files)

Version 1.0: 2012-08-08
Type: Initial release
Version 1.1: 2024-02-28
Changes: Data collection, Database references, Derived calculations

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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.