7KR8

Dihydrodipicolinate synthase (DHDPS) from C.jejuni, H56A mutant with pyruvate bound in the active site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

ALLOSTERIC SITE RESIDUE 'H56' CAPS THE INHIBITOR AT THE TIGHT DIMER INTERFACE FOR TRANSMITTING THE ALLOSTERIC INHIBITION SIGNALS IN Cj.DHDPS

Saran, S.Skovpen, Y.Yazdi, M.M.Palmer, D.R.J.Sanders, D.A.R.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
4-hydroxy-tetrahydrodipicolinate synthaseA, B, C, D, E, F310Campylobacter 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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PGE (Subject of Investigation/LOI)
Query on PGE

Download Ideal Coordinates CCD File 
FA [auth D], GA [auth D], I [auth A], N [auth B], QA [auth F], RA [auth F], V [auth C]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
PEG (Subject of Investigation/LOI)
Query on PEG

Download Ideal Coordinates CCD File 
JA [auth D], P [auth B], Q [auth B], SA [auth F], Y [auth C]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
EDO (Subject of Investigation/LOI)
Query on EDO

Download Ideal Coordinates CCD File 
CA [auth D] , DA [auth D] , EA [auth D] , G [auth A] , H [auth A] , M [auth B] , MA [auth E] , PA [auth F] , 
CA [auth D], DA [auth D], EA [auth D], G [auth A], H [auth A], M [auth B], MA [auth E], PA [auth F], S [auth C], T [auth C], U [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
ACT (Subject of Investigation/LOI)
Query on ACT

Download Ideal Coordinates CCD File 
HA [auth D] , IA [auth D] , J [auth A] , K [auth A] , NA [auth E] , O [auth B] , OA [auth E] , W [auth C] , 
HA [auth D], IA [auth D], J [auth A], K [auth A], NA [auth E], O [auth B], OA [auth E], W [auth C], X [auth C]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
AA [auth D], BA [auth D], KA [auth E], L [auth B], LA [auth E], R [auth C], Z [auth D]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
KPI
Query on KPI
A, B, C, D, E, FL-PEPTIDE LINKINGC9 H16 N2 O4LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.93α = 90
b = 231.65β = 90
c = 200.17γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
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: 2021-11-24
    Type: Initial release