7KH4

Dihydrodipicolinate synthase (DHDPS) from C.jejuni, H56W mutant with pyruvate bound in the active site and R,R-bislysine bound at the allosteric site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.157 
  • 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 1.2 of the entry. See complete history


Literature

Fluorescence-based Assay Development for Screening Novel Inhibitors of Dihydrodipicolinate Synthase from Campylobacter jejuni

Majdi Yazd, M.Reddy Annadi, K.Saran, S.Bhagwat, A.Sanders, D.A.R.Palmer, D.R.J.

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 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3VN (Subject of Investigation/LOI)
Query on 3VN

Download Ideal Coordinates CCD File 
AA [auth B],
BB [auth D],
G [auth A]
(2R,5R)-2,5-diamino-2,5-bis(4-aminobutyl)hexanedioic acid
C14 H30 N4 O4
XYUHPPVEDOOPDE-ZIAGYGMSSA-N
PG4 (Subject of Investigation/LOI)
Query on PG4

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DB [auth D]
EA [auth B]
IC [auth F]
L [auth A]
SA [auth C]
DB [auth D],
EA [auth B],
IC [auth F],
L [auth A],
SA [auth C],
UB [auth E]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE (Subject of Investigation/LOI)
Query on PGE

Download Ideal Coordinates CCD File 
DC [auth E],
NB [auth D],
OB [auth D],
PA [auth B]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG (Subject of Investigation/LOI)
Query on PEG

Download Ideal Coordinates CCD File 
BC [auth E]
IB [auth D]
KA [auth B]
LA [auth B]
LC [auth F]
BC [auth E],
IB [auth D],
KA [auth B],
LA [auth B],
LC [auth F],
MA [auth B],
MC [auth F],
W [auth A],
X [auth A],
ZA [auth C]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL (Subject of Investigation/LOI)
Query on GOL

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

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AC [auth E]
EB [auth D]
FA [auth B]
FB [auth D]
GA [auth B]
AC [auth E],
EB [auth D],
FA [auth B],
FB [auth D],
GA [auth B],
GB [auth D],
HA [auth B],
HB [auth D],
IA [auth B],
JA [auth B],
JC [auth F],
KC [auth F],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
TA [auth C],
U [auth A],
UA [auth C],
V [auth A],
VA [auth C],
VB [auth E],
WA [auth C],
WB [auth E],
XA [auth C],
XB [auth E],
YA [auth C],
YB [auth E],
ZB [auth E]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT (Subject of Investigation/LOI)
Query on ACT

Download Ideal Coordinates CCD File 
CC [auth E]
JB [auth D]
KB [auth D]
LB [auth D]
MB [auth D]
CC [auth E],
JB [auth D],
KB [auth D],
LB [auth D],
MB [auth D],
NA [auth B],
NC [auth F],
OA [auth B],
OC [auth F],
PC [auth F],
QC [auth F],
Y [auth A],
Z [auth A]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
BA [auth B]
CA [auth B]
CB [auth D]
DA [auth B]
EC [auth F]
BA [auth B],
CA [auth B],
CB [auth D],
DA [auth B],
EC [auth F],
FC [auth F],
GC [auth F],
H [auth A],
HC [auth F],
I [auth A],
J [auth A],
K [auth A],
PB [auth E],
QA [auth C],
QB [auth E],
RA [auth C],
RB [auth E],
SB [auth E],
TB [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: 1.75 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.158 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.41α = 90
b = 225.29β = 90
c = 199.41γ = 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: 2021-10-27
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Refinement description
  • Version 1.2: 2023-11-29
    Changes: Data collection