7KG2

Dihydrodipicolinate synthase (DHDPS) from C.jejuni, H59K mutant with pyruvate bound in the active site and L-histidine bound at the allosteric site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 

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

Reversing the roles of a crucial hydrogen-bonding pair: a lysine-insensitive mutant of Campylobacter jejuni dihydrodipicolinate synthase, H59K, binds histidine in its allosteric site

Majdi Yazdi, M.M.Saran, S.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 jejuniMutation(s): 1 
Gene Names: dapA
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
PG4 (Subject of Investigation/LOI)
Query on PG4

Download Ideal Coordinates CCD File 
KB [auth D]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
HIS (Subject of Investigation/LOI)
Query on HIS

Download Ideal Coordinates CCD File 
FC [auth E]
JA [auth B]
OB [auth D]
OC [auth F]
TA [auth C]
FC [auth E],
JA [auth B],
OB [auth D],
OC [auth F],
TA [auth C],
W [auth A]
HISTIDINE
C6 H10 N3 O2
HNDVDQJCIGZPNO-YFKPBYRVSA-O
PGE (Subject of Investigation/LOI)
Query on PGE

Download Ideal Coordinates CCD File 
AC [auth E]
BC [auth E]
CC [auth E]
HA [auth B]
IA [auth B]
AC [auth E],
BC [auth E],
CC [auth E],
HA [auth B],
IA [auth B],
JB [auth D],
SA [auth C],
V [auth A]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG (Subject of Investigation/LOI)
Query on PEG

Download Ideal Coordinates CCD File 
DC [auth E],
EC [auth E],
LB [auth D],
MB [auth D],
NB [auth D]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO (Subject of Investigation/LOI)
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth B]
AB [auth D]
BA [auth B]
BB [auth D]
CB [auth D]
AA [auth B],
AB [auth D],
BA [auth B],
BB [auth D],
CB [auth D],
G [auth A],
GC [auth F],
H [auth A],
HC [auth F],
I [auth A],
IC [auth F],
J [auth A],
JC [auth F],
K [auth A],
KA [auth C],
L [auth A],
LA [auth C],
M [auth A],
MA [auth C],
NA [auth C],
OA [auth C],
PA [auth C],
PB [auth E],
QB [auth E],
RB [auth E],
SB [auth E],
TB [auth E],
UA [auth D],
UB [auth E],
VA [auth D],
VB [auth E],
WA [auth D],
X [auth B],
XA [auth D],
Y [auth B],
YA [auth D],
Z [auth B],
ZA [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT (Subject of Investigation/LOI)
Query on ACT

Download Ideal Coordinates CCD File 
EA [auth B]
FA [auth B]
GA [auth B]
GB [auth D]
HB [auth D]
EA [auth B],
FA [auth B],
GA [auth B],
GB [auth D],
HB [auth D],
IB [auth D],
LC [auth F],
MC [auth F],
NC [auth F],
RA [auth C],
S [auth A],
T [auth A],
U [auth A],
YB [auth E],
ZB [auth E]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
CA [auth B]
DA [auth B]
DB [auth D]
EB [auth D]
FB [auth D]
CA [auth B],
DA [auth B],
DB [auth D],
EB [auth D],
FB [auth D],
KC [auth F],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
QA [auth C],
R [auth A],
WB [auth E],
XB [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: 1.89 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.78α = 90
b = 230.74β = 90
c = 202.2γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
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: 2021-10-20
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Refinement description
  • Version 1.2: 2023-11-29
    Changes: Data collection