7KNZ

Dihydrodipicolinate synthase (DHDPS) from C.jejuni, E88A mutant with pyruvate bound in the active site and R,R-bislysine at the allosteric site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 

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

THE ALLOSTERIC SITE RESIDUE, E88 INTERACTS WITH THE INHIBITORS TO TRANSMIT THE ALLOSTERIC INHIBITION SIGNALS IN Cj.DHDPS BY FORMING A HYDROGEN BOND.

Saran, S.Majdi Yazdi, M.Chung, I.Sanders, D.A.R.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
4-hydroxy-tetrahydrodipicolinate synthase
A, B, C, D, E
A, B, C, D, E, F
310Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819Mutation(s): 1 
Gene Names: dapACj0806
EC: 4.3.3.7
UniProt
Find proteins for Q9PPB4 (Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168))
Explore Q9PPB4 
Go to UniProtKB:  Q9PPB4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9PPB4
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3VN (Subject of Investigation/LOI)
Query on 3VN

Download Ideal Coordinates CCD File 
IB [auth F],
OA [auth D],
T [auth B]
(2R,5R)-2,5-diamino-2,5-bis(4-aminobutyl)hexanedioic acid
C14 H30 N4 O4
XYUHPPVEDOOPDE-ZIAGYGMSSA-N
PGE (Subject of Investigation/LOI)
Query on PGE

Download Ideal Coordinates CCD File 
IA [auth C],
M [auth A],
SA [auth D],
Z [auth B]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG (Subject of Investigation/LOI)
Query on PEG

Download Ideal Coordinates CCD File 
DB [auth E]
EB [auth E]
FB [auth E]
L [auth A]
LB [auth F]
DB [auth E],
EB [auth E],
FB [auth E],
L [auth A],
LB [auth F],
MB [auth F],
NB [auth F],
X [auth B],
Y [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL (Subject of Investigation/LOI)
Query on GOL

Download Ideal Coordinates CCD File 
NA [auth C],
PB [auth F]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO (Subject of Investigation/LOI)
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth B]
BA [auth B]
CA [auth B]
DA [auth B]
GB [auth E]
AA [auth B],
BA [auth B],
CA [auth B],
DA [auth B],
GB [auth E],
HB [auth E],
JA [auth C],
KA [auth C],
LA [auth C],
MA [auth C],
N [auth A],
O [auth A],
OB [auth F],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
TA [auth D],
UA [auth D],
VA [auth D],
WA [auth D],
XA [auth D],
YA [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT (Subject of Investigation/LOI)
Query on ACT

Download Ideal Coordinates CCD File 
BB [auth E]
CB [auth E]
GA [auth C]
HA [auth C]
I [auth A]
BB [auth E],
CB [auth E],
GA [auth C],
HA [auth C],
I [auth A],
J [auth A],
JB [auth F],
K [auth A],
KB [auth F],
RA [auth D],
W [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
AB [auth E]
EA [auth C]
FA [auth C]
G [auth A]
H [auth A]
AB [auth E],
EA [auth C],
FA [auth C],
G [auth A],
H [auth A],
PA [auth D],
QA [auth D],
U [auth B],
V [auth B],
ZA [auth E]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
KPI
Query on KPI
A, B, C, D, E
A, B, C, D, E, F
L-PEPTIDE LINKINGC9 H16 N2 O4LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.12α = 90
b = 231.21β = 90
c = 200.12γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)Canada--

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-17
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Refinement description
  • Version 1.2: 2023-11-29
    Changes: Data collection