4WJ8 | pdb_00004wj8

Human Pyruvate Kinase M2 Mutant C424A

PDB DOI: https://doi.org/10.2210/pdb4WJ8/pdb

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

Deposited: 2014-09-29 Released: 2015-09-30
Deposition Author(s): Mitchell, T., Yuan, M., McNae, I., Morgan, H., Walkinshaw, M.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.87 Å
R-Value Free:
0.243 (Depositor), 0.240 (DCC)
R-Value Work:
0.200 (Depositor), 0.200 (DCC)
R-Value Observed:
0.202 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Human Pyruvate Kinase M2 Mutant C424A

Mitchell, T., Yuan, M., McNae, I., Morgan, H., Walkinshaw, M.D.

To be published.

Macromolecule Content

Total Structure Weight: 242.86 kDa
Atom Count: 16,112
Modelled Residue Count: 2,068
Deposited Residue Count: 2,204
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyruvate kinase PKM	A, B, C, D	551	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

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FBP Query on FBP Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain Q [auth C] MOL2 format, chain F [auth A] MOL2 format, chain Q [auth C] mmCIF format, chain F [auth A] mmCIF format, chain Q [auth C]	F [auth A], Q [auth C]	1,6-di-O-phosphono-beta-D-fructofuranose C₆ H₁₄ O₁₂ P₂ RNBGYGVWRKECFJ-ARQDHWQXSA-N		Interactions Focus chain F [auth A] Focus chain Q [auth C] Interactions & Density Focus chain F [auth A] Focus chain Q [auth C]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain X [auth D] MOL2 format, chain M [auth B] MOL2 format, chain X [auth D] mmCIF format, chain M [auth B] mmCIF format, chain X [auth D]	M [auth B], X [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain M [auth B] Focus chain X [auth D] Interactions & Density Focus chain M [auth B] Focus chain X [auth D]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain W [auth D] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain W [auth D] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain W [auth D]	J [auth A], K [auth A], W [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain W [auth D] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain W [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain BA [auth D] SDF format, chain I [auth A] SDF format, chain P [auth B] SDF format, chain U [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain P [auth B] MOL2 format, chain U [auth C] mmCIF format, chain AA [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain P [auth B] mmCIF format, chain U [auth C]	AA [auth D], BA [auth D], I [auth A], P [auth B], U [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain I [auth A] Focus chain P [auth B] Focus chain U [auth C] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain I [auth A] Focus chain P [auth B] Focus chain U [auth C]
OXD Query on OXD Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain L [auth B] SDF format, chain R [auth C] SDF format, chain V [auth D] MOL2 format, chain E [auth A] MOL2 format, chain L [auth B] MOL2 format, chain R [auth C] MOL2 format, chain V [auth D] mmCIF format, chain E [auth A] mmCIF format, chain L [auth B] mmCIF format, chain R [auth C] mmCIF format, chain V [auth D]	E [auth A], L [auth B], R [auth C], V [auth D]	OXALIC ACID C₂ H₂ O₄ MUBZPKHOEPUJKR-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain L [auth B] Focus chain R [auth C] Focus chain V [auth D] Interactions & Density Focus chain E [auth A] Focus chain L [auth B] Focus chain R [auth C] Focus chain V [auth D]
K Query on K Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain O [auth B] SDF format, chain T [auth C] SDF format, chain Z [auth D] MOL2 format, chain G [auth A] MOL2 format, chain O [auth B] MOL2 format, chain T [auth C] MOL2 format, chain Z [auth D] mmCIF format, chain G [auth A] mmCIF format, chain O [auth B] mmCIF format, chain T [auth C] mmCIF format, chain Z [auth D]	G [auth A], O [auth B], T [auth C], Z [auth D]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain O [auth B] Focus chain T [auth C] Focus chain Z [auth D] Interactions & Density Focus chain G [auth A] Focus chain O [auth B] Focus chain T [auth C] Focus chain Z [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain N [auth B] SDF format, chain S [auth C] SDF format, chain Y [auth D] MOL2 format, chain H [auth A] MOL2 format, chain N [auth B] MOL2 format, chain S [auth C] MOL2 format, chain Y [auth D] mmCIF format, chain H [auth A] mmCIF format, chain N [auth B] mmCIF format, chain S [auth C] mmCIF format, chain Y [auth D]	H [auth A], N [auth B], S [auth C], Y [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain N [auth B] Focus chain S [auth C] Focus chain Y [auth D] Interactions & Density Focus chain H [auth A] Focus chain N [auth B] Focus chain S [auth C] Focus chain Y [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.87 Å
R-Value Free: 0.243 (Depositor), 0.240 (DCC)
R-Value Work: 0.200 (Depositor), 0.200 (DCC)
R-Value Observed: 0.202 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.359	α = 90
b = 115.26	β = 114.43
c = 109.401	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-09-30

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-09-30
Type: Initial release
Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.2: 2024-01-10
Changes: Data collection, Database references, Refinement description, Structure summary