4IPT

The crystal structure of a short-chain dehydrogenases/reductase (ethylated) from Veillonella parvula DSM 2008


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.546 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

The crystal structure of a short-chain dehydrogenases/reductase (ethylated) from Veillonella parvula DSM 2008

Tan, K.Hatzos-Skintges, C.Clancy, S.Joachimiak, A.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NAD-dependent epimerase/dehydratase
A
221Veillonella parvula (strain ATCC 10790 / DSM 2008 / JCM 12972 / Te3)N/A
Find proteins for D1BQI7 (Veillonella parvula (strain ATCC 10790 / DSM 2008 / JCM 12972 / Te3))
Go to UniProtKB:  D1BQI7
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMT
Query on FMT

Download SDF File 
Download CCD File 
A
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
PG4
Query on PG4

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Download CCD File 
A
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

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Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
ELY
Query on ELY
A
L-peptide linkingC10 H22 N2 O2LYS
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.546 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.187 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 51.681α = 90.00
b = 60.758β = 90.00
c = 68.769γ = 90.00
Software Package:
Software NamePurpose
SHELXDphasing
HKL-3000data scaling
WARPmodel building
PHENIXrefinement
DMphasing
HKL-3000phasing
DMmodel building
SBC-Collectdata collection
MLPHAREphasing
ARPmodel building
HKL-3000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-02-06
    Type: Initial release