5VPS

Crystal structure of an SDR from Burkholderia ambifaria in complex with NADPH with a TCEP adduct


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.148 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal structure of an SDR from Burkholderia ambifaria in complex with NADPH with a TCEP adduct

Mayclin, S.J.Dranow, D.M.Lorimer, D.Edwards, T.E.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Short-chain dehydrogenase/reductase SDR
A
267Burkholderia ambifaria (strain MC40-6)Mutation(s): 0 
Find proteins for B1YU47 (Burkholderia ambifaria (strain MC40-6))
Go to UniProtKB:  B1YU47
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9G1
Query on 9G1

Download SDF File 
Download CCD File 
A
[(4~{S})-3-aminocarbonyl-1-[(2~{R},3~{R},4~{S},5~{R})-5-[[[[(2~{R},3~{R},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3-oxidanyl-4-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-3,4-bis(oxidanyl)oxolan-2-yl]piperidin-4-yl]-tris(3-hydroxy-3-oxopropyl)phosphanium
C30 H48 N7 O23 P4
KCEMQRAWVXDPSM-NLJDEQFRSA-O
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 64.090α = 90.00
b = 64.090β = 90.00
c = 119.170γ = 90.00
Software Package:
Software NamePurpose
Cootmodel building
XDSdata reduction
PDB_EXTRACTdata extraction
XSCALEdata scaling
MOLREPphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-05-24
    Type: Initial release