7KK1

Dihydrodipicolinate synthase (DHDPS) from C.jejuni, N84A mutant with pyruvate bound in the active site and L-lysine bound at the allosteric site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.170 

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

A TIGHT DIMER INTERFACE N84 RESIDUE, PLAYS A CRITICAL ROLE IN THE TRANSMISSION OF THE ALLOSTERIC INHIBITION SIGNALS IN Cj.DHDPS

Saran, S.Majdi Yazd, M.Palmer, D.R.J.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
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PGE (Subject of Investigation/LOI)
Query on PGE

Download Ideal Coordinates CCD File 
BB [auth D]
HA [auth B]
IB [auth E]
P [auth A]
RA [auth C]
BB [auth D],
HA [auth B],
IB [auth E],
P [auth A],
RA [auth C],
UB [auth F]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
LYS (Subject of Investigation/LOI)
Query on LYS

Download Ideal Coordinates CCD File 
CB [auth E]
G [auth A]
IA [auth C]
LB [auth F]
R [auth B]
CB [auth E],
G [auth A],
IA [auth C],
LB [auth F],
R [auth B],
TA [auth D]
LYSINE
C6 H15 N2 O2
KDXKERNSBIXSRK-YFKPBYRVSA-O
PEG (Subject of Investigation/LOI)
Query on PEG

Download Ideal Coordinates CCD File 
JB [auth E],
Q [auth A],
SA [auth C]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL (Subject of Investigation/LOI)
Query on GOL

Download Ideal Coordinates CCD File 
KB [auth E]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]
FB [auth E]
AA [auth B],
BA [auth B],
CA [auth B],
DA [auth B],
FB [auth E],
GB [auth E],
J [auth A],
K [auth A],
L [auth A],
LA [auth C],
M [auth A],
MA [auth C],
N [auth A],
NA [auth C],
O [auth A],
OB [auth F],
PB [auth F],
QB [auth F],
RB [auth F],
SB [auth F],
WA [auth D],
X [auth B],
XA [auth D],
Y [auth B],
YA [auth D],
Z [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT (Subject of Investigation/LOI)
Query on ACT

Download Ideal Coordinates CCD File 
AB [auth D]
EA [auth B]
FA [auth B]
GA [auth B]
HB [auth E]
AB [auth D],
EA [auth B],
FA [auth B],
GA [auth B],
HB [auth E],
OA [auth C],
PA [auth C],
QA [auth C],
TB [auth F],
ZA [auth D]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
DB [auth E]
EB [auth E]
H [auth A]
I [auth A]
JA [auth C]
DB [auth E],
EB [auth E],
H [auth A],
I [auth A],
JA [auth C],
KA [auth C],
MB [auth F],
NB [auth F],
S [auth B],
T [auth B],
U [auth B],
UA [auth D],
V [auth B],
VA [auth D],
W [auth B]
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: 1.77 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.170 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.69α = 90
b = 231.98β = 90
c = 200.45γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction
AMPLEphasing

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: 2021-11-03
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Refinement description
  • Version 1.2: 2023-11-29
    Changes: Data collection