7LBD

Dihydrodipicolinate synthase (DHDPS) from C.jejuni, H59K mutant with pyruvate bound in the active site in C2221 space group


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 

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

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 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 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PGE (Subject of Investigation/LOI)
Query on PGE

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

Download Ideal Coordinates CCD File 
AB [auth F]
FA [auth C]
GA [auth C]
MA [auth D]
O [auth A]
AB [auth F],
FA [auth C],
GA [auth C],
MA [auth D],
O [auth A],
P [auth A],
W [auth B],
YA [auth F],
ZA [auth F]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO (Subject of Investigation/LOI)
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth C]
HA [auth D]
I [auth A]
J [auth A]
K [auth A]
AA [auth C],
HA [auth D],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
NA [auth E],
OA [auth E],
PA [auth E],
S [auth B],
T [auth B],
U [auth B],
WA [auth F],
XA [auth F],
Y [auth C],
Z [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT (Subject of Investigation/LOI)
Query on ACT

Download Ideal Coordinates CCD File 
CA [auth C]
DA [auth C]
EA [auth C]
KA [auth D]
LA [auth D]
CA [auth C],
DA [auth C],
EA [auth C],
KA [auth D],
LA [auth D],
N [auth A],
RA [auth E],
SA [auth E],
TA [auth E],
UA [auth E]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
Q [auth B]
R [auth B]
VA [auth F]
G [auth A],
H [auth A],
Q [auth B],
R [auth B],
VA [auth F],
X [auth C]
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: 1.99 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.12α = 90
b = 232.14β = 90
c = 201.81γ = 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: 2022-01-12
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Refinement description
  • Version 1.2: 2023-11-29
    Changes: Data collection