3SRD | pdb_00003srd

Human M2 pyruvate kinase in complex with fructose 1-6 bisphosphate and Oxalate.

PDB DOI: https://doi.org/10.2210/pdb3SRD/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: 2.90 Å
R-Value Free:
0.279 (Depositor), 0.271 (DCC)
R-Value Work:
0.253 (Depositor), 0.249 (DCC)
R-Value Observed:
0.254 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 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: 243.14 kDa
Atom Count: 16,047
Modeled Residue Count: 2,056
Deposited Residue Count: 2,204
Unique protein chains: 1

Macromolecules

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| 3D Structure

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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FBP Query on FBP Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain N [auth C] SDF format, chain S [auth D] SDF format, chain F [auth A] MOL2 format, chain L [auth B] MOL2 format, chain N [auth C] MOL2 format, chain S [auth D] MOL2 format, chain F [auth A] mmCIF format, chain L [auth B] mmCIF format, chain N [auth C] mmCIF format, chain S [auth D] mmCIF format, chain F [auth A]	F [auth A], L [auth B], N [auth C], S [auth D]	1,6-di-O-phosphono-beta-D-fructofuranose C₆ H₁₄ O₁₂ P₂ RNBGYGVWRKECFJ-ARQDHWQXSA-N		Interactions Focus chain F [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain S [auth D] Interactions & Density Focus chain F [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain S [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain R [auth C] SDF format, chain X [auth D] SDF format, chain W [auth D] SDF format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain R [auth C] MOL2 format, chain X [auth D] MOL2 format, chain W [auth D] MOL2 format, chain I [auth A] mmCIF format, chain M [auth B] mmCIF format, chain R [auth C] mmCIF format, chain X [auth D] mmCIF format, chain W [auth D] mmCIF format, chain I [auth A]	I [auth A], M [auth B], R [auth C], W [auth D], X [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain M [auth B] Focus chain R [auth C] Focus chain W [auth D] Focus chain X [auth D] Interactions & Density Focus chain I [auth A] Focus chain M [auth B] Focus chain R [auth C] Focus chain W [auth D] Focus chain X [auth D]
OXL Query on OXL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain T [auth D] SDF format, chain O [auth C] SDF format, chain J [auth B] MOL2 format, chain E [auth A] MOL2 format, chain T [auth D] MOL2 format, chain O [auth C] MOL2 format, chain J [auth B] mmCIF format, chain E [auth A] mmCIF format, chain T [auth D] mmCIF format, chain O [auth C] mmCIF format, chain J [auth B]	E [auth A], J [auth B], O [auth C], T [auth D]	OXALATE ION C₂ O₄ MUBZPKHOEPUJKR-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain O [auth C] Focus chain T [auth D] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain O [auth C] Focus chain T [auth D]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain V [auth D] SDF format, chain Q [auth C] MOL2 format, chain G [auth A] MOL2 format, chain V [auth D] MOL2 format, chain Q [auth C] mmCIF format, chain G [auth A] mmCIF format, chain V [auth D] mmCIF format, chain Q [auth C]	G [auth A], Q [auth C], V [auth D]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain Q [auth C] Focus chain V [auth D] Interactions & Density Focus chain G [auth A] Focus chain Q [auth C] Focus chain V [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain P [auth C] SDF format, chain U [auth D] SDF format, chain K [auth B] MOL2 format, chain H [auth A] MOL2 format, chain P [auth C] MOL2 format, chain U [auth D] MOL2 format, chain K [auth B] mmCIF format, chain H [auth A] mmCIF format, chain P [auth C] mmCIF format, chain U [auth D] mmCIF format, chain K [auth B]	H [auth A], K [auth B], P [auth C], U [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain K [auth B] Focus chain P [auth C] Focus chain U [auth D] Interactions & Density Focus chain H [auth A] Focus chain K [auth B] Focus chain P [auth C] Focus chain U [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.279 (Depositor), 0.271 (DCC)
R-Value Work: 0.253 (Depositor), 0.249 (DCC)
R-Value Observed: 0.254 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.05	α = 90
b = 117.37	β = 113.56
c = 110.46	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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Ligand Structure Quality Assessment

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: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations, Structure summary
Version 1.2: 2024-02-28
Changes: Data collection, Database references, Structure summary