6V74

Crystal Structure of Human PKM2 in Complex with L-asparagine

PDB DOI: https://doi.org/10.2210/pdb6V74/pdb

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

Deposited: 2019-12-07 Released: 2020-03-18
Deposition Author(s): Nandi, S., Dey, M.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.32 Å
R-Value Free: 0.275
R-Value Work: 0.233
R-Value Observed: 0.235

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 244.06 kDa
Atom Count: 14,426
Modelled Residue Count: 1,955
Deposited Residue Count: 2,200
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	550	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 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FBP Query on FBP Download Ideal Coordinates CCD File SDF format, chain IA [auth C] SDF format, chain J [auth A] SDF format, chain LA [auth D] SDF format, chain S [auth B] MOL2 format, chain IA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain LA [auth D] MOL2 format, chain S [auth B]	IA [auth C], J [auth A], LA [auth D], S [auth B]	1,6-di-O-phosphono-beta-D-fructofuranose C₆ H₁₄ O₁₂ P₂ RNBGYGVWRKECFJ-ARQDHWQXSA-N		Interactions Focus chain IA [auth C] Focus chain J [auth A] Focus chain LA [auth D] Focus chain S [auth B] Interactions & Density Focus chain IA [auth C] Focus chain J [auth A] Focus chain LA [auth D] Focus chain S [auth B]
ASN (Subject of Investigation/LOI) Query on ASN Download Ideal Coordinates CCD File SDF format, chain X [auth C] MOL2 format, chain X [auth C]	X [auth C]	ASPARAGINE C₄ H₈ N₂ O₃ DCXYFEDJOCDNAF-REOHCLBHSA-N		Interactions Focus chain X [auth C] Interactions & Density Focus chain X [auth C]
144 Query on 144 Download Ideal Coordinates CCD File SDF format, chain OA [auth D] MOL2 format, chain OA [auth D]	OA [auth D]	TRIS-HYDROXYMETHYL-METHYL-AMMONIUM C₄ H₁₂ N O₃ DRDCQJADRSJFFD-UHFFFAOYSA-N		Interactions Focus chain OA [auth D] Interactions & Density Focus chain OA [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth C] SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain EA [auth C] SDF format, chain FA [auth C] SDF format, chain G [auth A] SDF format, chain GA [auth C] SDF format, chain H [auth A] SDF format, chain JA [auth D] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain Y [auth C] SDF format, chain Z [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth C] MOL2 format, chain H [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C]	AA [auth C] BA [auth C] CA [auth C] DA [auth C] EA [auth C] AA [auth C], BA [auth C], CA [auth C], DA [auth C], EA [auth C], FA [auth C], G [auth A], GA [auth C], H [auth A], JA [auth D], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B], Y [auth C], Z [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain G [auth A] Focus chain GA [auth C] Focus chain H [auth A] Focus chain JA [auth D] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain G [auth A] Focus chain GA [auth C] Focus chain H [auth A] Focus chain JA [auth D] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain Y [auth C] Focus chain Z [auth C]
OXL Query on OXL Download Ideal Coordinates CCD File SDF format, chain HA [auth C] SDF format, chain I [auth A] SDF format, chain KA [auth D] SDF format, chain R [auth B] MOL2 format, chain HA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain R [auth B]	HA [auth C], I [auth A], KA [auth D], R [auth B]	OXALATE ION C₂ O₄ MUBZPKHOEPUJKR-UHFFFAOYSA-L		Interactions Focus chain HA [auth C] Focus chain I [auth A] Focus chain KA [auth D] Focus chain R [auth B] Interactions & Density Focus chain HA [auth C] Focus chain I [auth A] Focus chain KA [auth D] Focus chain R [auth B]
K Query on K Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain U [auth C] SDF format, chain V [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C]	E [auth A], F [auth A], U [auth C], V [auth C]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain U [auth C] Focus chain V [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain U [auth C] Focus chain V [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain W [auth C] MOL2 format, chain L [auth B] MOL2 format, chain W [auth C]	L [auth B], W [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain L [auth B] Focus chain W [auth C] Interactions & Density Focus chain L [auth B] Focus chain W [auth C]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain MA [auth D] SDF format, chain NA [auth D] SDF format, chain T [auth B] MOL2 format, chain K [auth A] MOL2 format, chain MA [auth D] MOL2 format, chain NA [auth D] MOL2 format, chain T [auth B]	K [auth A], MA [auth D], NA [auth D], T [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain T [auth B] Interactions & Density Focus chain K [auth A] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain T [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
ASN	Binding MOAD: 6V74	Kd: 2.70e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.32 Å
R-Value Free: 0.275
R-Value Work: 0.233
R-Value Observed: 0.235
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.99	α = 90
b = 154.58	β = 102.54
c = 92.15	γ = 90

Software Package:

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

Structure Validation

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Currently 6V74 does not have a validation slider image.

Entry History & Funding Information

Deposition Data

Released Date: 2020-03-18

Deposition Author(s):

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: 2020-03-18
Type: Initial release
Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.2: 2020-09-30
Changes: Database references, Structure summary
Version 1.3: 2023-10-11
Changes: Data collection, Database references, Refinement description