5KSW

DHODB-I74D mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.47 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Isoleucine 74 Plays a Key Role in Controlling Electron Transfer Between Lactococcus lactis Dihydroorotate Dehydrogenase 1B Subunits

Pompeu, Y.A.Stewart, J.D.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Dihydroorotate dehydrogenaseA,
D [auth C]
306Lactococcus lactisMutation(s): 1 
Gene Names: pyrDLG36_1039
EC: 1.3.1.14
UniProt
Find proteins for Q9CFW8 (Lactococcus lactis subsp. lactis (strain IL1403))
Explore Q9CFW8 
Go to UniProtKB:  Q9CFW8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9CFW8
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Dihydroorotate dehydrogenase B (NAD(+)), electron transfer subunitB,
C [auth D]
262Lactococcus lactis subsp. lactisMutation(s): 0 
Gene Names: pyrKNCDO895_2366
UniProt
Find proteins for Q9CFW7 (Lactococcus lactis subsp. lactis (strain IL1403))
Explore Q9CFW7 
Go to UniProtKB:  Q9CFW7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9CFW7
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
H [auth B],
K [auth D]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
FMN
Query on FMN

Download Ideal Coordinates CCD File 
E [auth A],
M [auth C]
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
FES
Query on FES

Download Ideal Coordinates CCD File 
I [auth B],
L [auth D]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
G [auth A],
N [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.47 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.179 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.99α = 90
b = 151.72β = 90
c = 214.31γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PHASERphasing
PDB_EXTRACTdata extraction
iMOSFLMdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-03
    Type: Initial release
  • Version 1.1: 2016-08-10
    Changes: Data collection
  • Version 1.2: 2017-04-26
    Changes: Structure summary
  • Version 1.3: 2017-09-27
    Changes: Author supporting evidence
  • Version 1.4: 2017-11-01
    Changes: Author supporting evidence