8F6M

Complex of Rabbit muscle pyruvate kinase with ADP and the phosphonate analogue of PEP mimicking the Michaelis complex.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.158 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

PYK-SubstitutionOME: an integrated database containing allosteric coupling, ligand affinity and mutational, structural, pathological, bioinformatic and computational information about pyruvate kinase isozymes.

Swint-Kruse, L.Dougherty, L.L.Page, B.Wu, T.O'Neil, P.T.Prasannan, C.B.Timmons, C.Tang, Q.Parente, D.J.Sreenivasan, S.Holyoak, T.Fenton, A.W.

(2023) Database (Oxford) 2023

  • DOI: https://doi.org/10.1093/database/baad030
  • Primary Citation of Related Structures:  
    8F5T, 8F5U, 8F6M

  • PubMed Abstract: 

    Interpreting changes in patient genomes, understanding how viruses evolve and engineering novel protein function all depend on accurately predicting the functional outcomes that arise from amino acid substitutions. To that end, the development of first-generation prediction algorithms was guided by historic experimental datasets. However, these datasets were heavily biased toward substitutions at positions that have not changed much throughout evolution (i.e. conserved). Although newer datasets include substitutions at positions that span a range of evolutionary conservation scores, these data are largely derived from assays that agglomerate multiple aspects of function. To facilitate predictions from the foundational chemical properties of proteins, large substitution databases with biochemical characterizations of function are needed. We report here a database derived from mutational, biochemical, bioinformatic, structural, pathological and computational studies of a highly studied protein family-pyruvate kinase (PYK). A centerpiece of this database is the biochemical characterization-including quantitative evaluation of allosteric regulation-of the changes that accompany substitutions at positions that sample the full conservation range observed in the PYK family. We have used these data to facilitate critical advances in the foundational studies of allosteric regulation and protein evolution and as rigorous benchmarks for testing protein predictions. We trust that the collected dataset will be useful for the broader scientific community in the further development of prediction algorithms. Database URL https://github.com/djparente/PYK-DB.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pyruvate kinase PKM
A, B, C, D, E
A, B, C, D, E, F, G, H
531Oryctolagus cuniculusMutation(s): 1 
EC: 2.7.1.40 (PDB Primary Data), 2.7.11.1 (PDB Primary Data), 2.7.10.2 (PDB Primary Data)
UniProt
Find proteins for P11974 (Oryctolagus cuniculus)
Explore P11974 
Go to UniProtKB:  P11974
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11974
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
DA [auth C],
HB [auth F],
I [auth A],
PA [auth D],
T [auth B]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
GZ3 (Subject of Investigation/LOI)
Query on GZ3

Download Ideal Coordinates CCD File 
AC [auth H],
IB [auth F],
TB [auth G],
XA [auth E]
(E)-2-METHYL-3-PHOSPHONOACRYLATE
C4 H7 O5 P
XGDAHZFVQMTYCT-NSCUHMNNSA-N
SIN (Subject of Investigation/LOI)
Query on SIN

Download Ideal Coordinates CCD File 
BB [auth E]
DC [auth H]
EA [auth C]
IA [auth C]
J [auth A]
BB [auth E],
DC [auth H],
EA [auth C],
IA [auth C],
J [auth A],
MB [auth F],
N [auth A],
QA [auth D],
U [auth B],
UA [auth D],
WB [auth G],
Y [auth B]
SUCCINIC ACID
C4 H6 O4
KDYFGRWQOYBRFD-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth B]
BA [auth B]
CA [auth B]
DB [auth E]
EB [auth E]
AA [auth B],
BA [auth B],
CA [auth B],
DB [auth E],
EB [auth E],
FB [auth E],
FC [auth H],
GB [auth E],
GC [auth H],
KA [auth C],
LA [auth C],
MA [auth C],
NA [auth C],
OA [auth C],
OB [auth F],
P [auth A],
PB [auth F],
Q [auth A],
QB [auth F],
R [auth A],
RB [auth F],
S [auth A],
SB [auth F],
WA [auth D],
YB [auth G],
ZB [auth G]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ALA (Subject of Investigation/LOI)
Query on ALA

Download Ideal Coordinates CCD File 
CB [auth E]
EC [auth H]
JA [auth C]
NB [auth F]
O [auth A]
CB [auth E],
EC [auth H],
JA [auth C],
NB [auth F],
O [auth A],
VA [auth D],
XB [auth G],
Z [auth B]
ALANINE
C3 H7 N O2
QNAYBMKLOCPYGJ-REOHCLBHSA-N
MN
Query on MN

Download Ideal Coordinates CCD File 
BC [auth H]
FA [auth C]
GA [auth C]
HC [auth H]
JB [auth F]
BC [auth H],
FA [auth C],
GA [auth C],
HC [auth H],
JB [auth F],
K [auth A],
KB [auth F],
L [auth A],
RA [auth D],
SA [auth D],
UB [auth G],
V [auth B],
X [auth B],
YA [auth E],
ZA [auth E]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
AB [auth E]
CC [auth H]
HA [auth C]
LB [auth F]
M [auth A]
AB [auth E],
CC [auth H],
HA [auth C],
LB [auth F],
M [auth A],
TA [auth D],
VB [auth G],
W [auth B]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.158 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.026α = 90
b = 216.396β = 90
c = 258.151γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-24
    Type: Initial release
  • Version 1.1: 2023-10-25
    Changes: Data collection, Refinement description