6NU1

Crystal Structure of Human PKM2 in Complex with L-cysteine

PDB DOI: https://doi.org/10.2210/pdb6NU1/pdb

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

Deposited: 2019-01-30 Released: 2019-08-21
Deposition Author(s): Srivastava, D., Nandi, S., Dey, M.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.235
R-Value Work: 0.191
R-Value Observed: 0.193

wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 243.13 kDa
Atom Count: 15,092
Modelled Residue Count: 1,959
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): 0 Gene Names: PKM, OIP3, PK2, PK3, PKM2 EC: 2.7.1.40
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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FBP Query on FBP Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain O [auth C] SDF format, chain S [auth D] SDF format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain O [auth C] MOL2 format, chain S [auth D] MOL2 format, chain F [auth A]	F [auth A], J [auth B], O [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 J [auth B] Focus chain O [auth C] Focus chain S [auth D] Interactions & Density Focus chain F [auth A] Focus chain J [auth B] Focus chain O [auth C] Focus chain S [auth D]
CYS Query on CYS Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain N [auth C] SDF format, chain R [auth D] SDF format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain N [auth C] MOL2 format, chain R [auth D] MOL2 format, chain E [auth A]	E [auth A], I [auth B], N [auth C], R [auth D]	CYSTEINE C₃ H₇ N O₂ S XUJNEKJLAYXESH-REOHCLBHSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain N [auth C] Focus chain R [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain N [auth C] Focus chain R [auth D]
OXL Query on OXL Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain Q [auth C] SDF format, chain U [auth D] SDF format, chain L [auth B] MOL2 format, chain H [auth A] MOL2 format, chain Q [auth C] MOL2 format, chain U [auth D] MOL2 format, chain L [auth B]	H [auth A], L [auth B], Q [auth C], U [auth D]	OXALATE ION C₂ O₄ MUBZPKHOEPUJKR-UHFFFAOYSA-L		Interactions Focus chain H [auth A] Focus chain L [auth B] Focus chain Q [auth C] Focus chain U [auth D] Interactions & Density Focus chain H [auth A] Focus chain L [auth B] Focus chain Q [auth C] Focus chain U [auth D]
K Query on K Download Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain V [auth D] MOL2 format, chain M [auth B] MOL2 format, chain V [auth D]	M [auth B], V [auth D]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain M [auth B] Focus chain V [auth D] Interactions & Density Focus chain M [auth B] Focus chain V [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain G [auth A] SDF format, chain P [auth C] SDF format, chain T [auth D] MOL2 format, chain K [auth B] MOL2 format, chain G [auth A] MOL2 format, chain P [auth C] MOL2 format, chain T [auth D]	G [auth A], K [auth B], P [auth C], T [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain K [auth B] Focus chain P [auth C] Focus chain T [auth D] Interactions & Density Focus chain G [auth A] Focus chain K [auth B] Focus chain P [auth C] Focus chain T [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.235
R-Value Work: 0.191
R-Value Observed: 0.193
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.829	α = 90
b = 155.918	β = 103.51
c = 94.136	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing
Coot	model building

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2019-08-21

Deposition Author(s):

Srivastava, D.

Nandi, S.

Dey, M.

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	CLP 1506181

Revision History (Full details and data files)

Version 1.0: 2019-08-21
Type: Initial release
Version 1.1: 2019-09-18
Changes: Data collection, Database references
Version 1.2: 2019-11-27
Changes: Author supporting evidence
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.4: 2023-10-11
Changes: Data collection, Database references, Refinement description, Structure summary

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Help and Resources

6NU1

Crystal Structure of Human PKM2 in Complex with L-cysteine

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)