3SRF | pdb_00003srf

Human M1 pyruvate kinase

PDB DOI: https://doi.org/10.2210/pdb3SRF/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
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: 2.85 Å
R-Value Free:
0.280 (Depositor), 0.278 (DCC)
R-Value Work:
0.221 (Depositor), 0.221 (DCC)
R-Value Observed:
0.224 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 2.0 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: 485.22 kDa
Atom Count: 32,320
Modeled Residue Count: 4,128
Deposited Residue Count: 4,408
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 [auth C] B [auth A] C [auth B] D E A [auth C], B [auth A], C [auth B], D, E, F, G, H	551	Homo sapiens	Mutation(s): 0 Gene Names: OIP3, PK2, PK3, PKM, PKM1, 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
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain X [auth D] SDF format, chain SA [auth H] SDF format, chain S [auth B] SDF format, chain NA [auth G] SDF format, chain N [auth A] SDF format, chain I [auth C] SDF format, chain HA [auth F] SDF format, chain CA [auth E] MOL2 format, chain X [auth D] MOL2 format, chain SA [auth H] MOL2 format, chain S [auth B] MOL2 format, chain NA [auth G] MOL2 format, chain N [auth A] MOL2 format, chain I [auth C] MOL2 format, chain HA [auth F] MOL2 format, chain CA [auth E] mmCIF format, chain X [auth D] mmCIF format, chain SA [auth H] mmCIF format, chain S [auth B] mmCIF format, chain NA [auth G] mmCIF format, chain N [auth A] mmCIF format, chain I [auth C] mmCIF format, chain HA [auth F] mmCIF format, chain CA [auth E]	CA [auth E] HA [auth F] I [auth C] N [auth A] NA [auth G] CA [auth E], HA [auth F], I [auth C], N [auth A], NA [auth G], S [auth B], SA [auth H], X [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain CA [auth E] Focus chain HA [auth F] Focus chain I [auth C] Focus chain N [auth A] Focus chain NA [auth G] Focus chain S [auth B] Focus chain SA [auth H] Focus chain X [auth D] Interactions & Density Focus chain CA [auth E] Focus chain HA [auth F] Focus chain I [auth C] Focus chain N [auth A] Focus chain NA [auth G] Focus chain S [auth B] Focus chain SA [auth H] Focus chain X [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain W [auth B] SDF format, chain RA [auth G] SDF format, chain R [auth A] SDF format, chain MA [auth F] SDF format, chain M [auth C] SDF format, chain LA [auth F] SDF format, chain GA [auth E] SDF format, chain BA [auth D] MOL2 format, chain W [auth B] MOL2 format, chain RA [auth G] MOL2 format, chain R [auth A] MOL2 format, chain MA [auth F] MOL2 format, chain M [auth C] MOL2 format, chain LA [auth F] MOL2 format, chain GA [auth E] MOL2 format, chain BA [auth D] mmCIF format, chain W [auth B] mmCIF format, chain RA [auth G] mmCIF format, chain R [auth A] mmCIF format, chain MA [auth F] mmCIF format, chain M [auth C] mmCIF format, chain LA [auth F] mmCIF format, chain GA [auth E] mmCIF format, chain BA [auth D]	BA [auth D] GA [auth E] LA [auth F] M [auth C] MA [auth F] BA [auth D], GA [auth E], LA [auth F], M [auth C], MA [auth F], R [auth A], RA [auth G], W [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain GA [auth E] Focus chain LA [auth F] Focus chain M [auth C] Focus chain MA [auth F] Focus chain R [auth A] Focus chain RA [auth G] Focus chain W [auth B] Interactions & Density Focus chain BA [auth D] Focus chain GA [auth E] Focus chain LA [auth F] Focus chain M [auth C] Focus chain MA [auth F] Focus chain R [auth A] Focus chain RA [auth G] Focus chain W [auth B]
PYR Query on PYR Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain FA [auth E] SDF format, chain KA [auth F] SDF format, chain L [auth C] SDF format, chain Q [auth A] SDF format, chain QA [auth G] SDF format, chain V [auth B] SDF format, chain VA [auth H] MOL2 format, chain AA [auth D] MOL2 format, chain FA [auth E] MOL2 format, chain KA [auth F] MOL2 format, chain L [auth C] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth G] MOL2 format, chain V [auth B] MOL2 format, chain VA [auth H] mmCIF format, chain AA [auth D] mmCIF format, chain FA [auth E] mmCIF format, chain KA [auth F] mmCIF format, chain L [auth C] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth G] mmCIF format, chain V [auth B] mmCIF format, chain VA [auth H]	AA [auth D] FA [auth E] KA [auth F] L [auth C] Q [auth A] AA [auth D], FA [auth E], KA [auth F], L [auth C], Q [auth A], QA [auth G], V [auth B], VA [auth H]	PYRUVIC ACID C₃ H₄ O₃ LCTONWCANYUPML-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain FA [auth E] Focus chain KA [auth F] Focus chain L [auth C] Focus chain Q [auth A] Focus chain QA [auth G] Focus chain V [auth B] Focus chain VA [auth H] Interactions & Density Focus chain AA [auth D] Focus chain FA [auth E] Focus chain KA [auth F] Focus chain L [auth C] Focus chain Q [auth A] Focus chain QA [auth G] Focus chain V [auth B] Focus chain VA [auth H]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain Y [auth D] SDF format, chain TA [auth H] SDF format, chain T [auth B] SDF format, chain OA [auth G] SDF format, chain O [auth A] SDF format, chain J [auth C] SDF format, chain IA [auth F] SDF format, chain DA [auth E] MOL2 format, chain Y [auth D] MOL2 format, chain TA [auth H] MOL2 format, chain T [auth B] MOL2 format, chain OA [auth G] MOL2 format, chain O [auth A] MOL2 format, chain J [auth C] MOL2 format, chain IA [auth F] MOL2 format, chain DA [auth E] mmCIF format, chain Y [auth D] mmCIF format, chain TA [auth H] mmCIF format, chain T [auth B] mmCIF format, chain OA [auth G] mmCIF format, chain O [auth A] mmCIF format, chain J [auth C] mmCIF format, chain IA [auth F] mmCIF format, chain DA [auth E]	DA [auth E] IA [auth F] J [auth C] O [auth A] OA [auth G] DA [auth E], IA [auth F], J [auth C], O [auth A], OA [auth G], T [auth B], TA [auth H], Y [auth D]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain DA [auth E] Focus chain IA [auth F] Focus chain J [auth C] Focus chain O [auth A] Focus chain OA [auth G] Focus chain T [auth B] Focus chain TA [auth H] Focus chain Y [auth D] Interactions & Density Focus chain DA [auth E] Focus chain IA [auth F] Focus chain J [auth C] Focus chain O [auth A] Focus chain OA [auth G] Focus chain T [auth B] Focus chain TA [auth H] Focus chain Y [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain UA [auth H] SDF format, chain Z [auth D] SDF format, chain U [auth B] SDF format, chain PA [auth G] SDF format, chain P [auth A] SDF format, chain K [auth C] SDF format, chain JA [auth F] SDF format, chain EA [auth E] MOL2 format, chain UA [auth H] MOL2 format, chain Z [auth D] MOL2 format, chain U [auth B] MOL2 format, chain PA [auth G] MOL2 format, chain P [auth A] MOL2 format, chain K [auth C] MOL2 format, chain JA [auth F] MOL2 format, chain EA [auth E] mmCIF format, chain UA [auth H] mmCIF format, chain Z [auth D] mmCIF format, chain U [auth B] mmCIF format, chain PA [auth G] mmCIF format, chain P [auth A] mmCIF format, chain K [auth C] mmCIF format, chain JA [auth F] mmCIF format, chain EA [auth E]	EA [auth E] JA [auth F] K [auth C] P [auth A] PA [auth G] EA [auth E], JA [auth F], K [auth C], P [auth A], PA [auth G], U [auth B], UA [auth H], Z [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain EA [auth E] Focus chain JA [auth F] Focus chain K [auth C] Focus chain P [auth A] Focus chain PA [auth G] Focus chain U [auth B] Focus chain UA [auth H] Focus chain Z [auth D] Interactions & Density Focus chain EA [auth E] Focus chain JA [auth F] Focus chain K [auth C] Focus chain P [auth A] Focus chain PA [auth G] Focus chain U [auth B] Focus chain UA [auth H] Focus chain Z [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.85 Å
R-Value Free: 0.280 (Depositor), 0.278 (DCC)
R-Value Work: 0.221 (Depositor), 0.221 (DCC)
R-Value Observed: 0.224 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 238.003	α = 90
b = 192.222	β = 89.999
c = 109.06	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

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 2.0: 2023-11-15
Changes: Atomic model, Data collection, Database references, Derived calculations