2G8Y

The structure of a putative malate/lactate dehydrogenase from E. coli.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.159 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

The structure of a putative malate/lactate dehydrogenase from E. coli.

Cuff, M.E.Skarina, T.Edwards, A.Savchenko, A.Cymborowski, M.Minor, W.Joachimiak, A.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Malate/L-lactate dehydrogenasesA, B385Escherichia coli K-12Mutation(s): 9 
Gene Names: ybiChcxBb0801JW0786
EC: 1.1.1 (UniProt), 1.1.1.237 (UniProt)
UniProt
Find proteins for P30178 (Escherichia coli (strain K12))
Explore P30178 
Go to UniProtKB:  P30178
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP30178
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download Ideal Coordinates CCD File 
F [auth A],
R [auth B]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
L [auth A]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A],
M [auth B],
N [auth B],
C [auth A],
D [auth A],
E [auth A],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
Q [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
S [auth B],
T [auth B],
U [auth B],
V [auth B],
W [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.159 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 139.095α = 90
b = 139.095β = 90
c = 151.654γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
SBC-Collectdata collection
HKL-2000data scaling
HKL-3000phasing
SHELXphasing
MLPHAREphasing
DMphasing
RESOLVEphasing
ARP/wARPmodel building
Omodel building
Cootmodel building

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-04-25
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Source and taxonomy, Version format compliance
  • Version 1.3: 2022-04-13
    Changes: Database references, Derived calculations, Structure summary