6NA4

Co crystal structure of ECR with Butryl-CoA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.170 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative crotonyl-CoA reductase
A, B, C, D
448Kitasatospora setae KM-6054Mutation(s): 0 
Gene Names: ccr1KSE_56510
UniProt
Find proteins for E4N096 (Kitasatospora setae (strain ATCC 33774 / DSM 43861 / JCM 3304 / KCC A-0304 / NBRC 14216 / KM-6054))
Explore E4N096 
Go to UniProtKB:  E4N096
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE4N096
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
YAS
Query on YAS

Download Ideal Coordinates CCD File 
K [auth C],
O [auth D]
~{S}-[2-[3-[[(2~{R})-4-[[[(2~{S},3~{R},4~{S},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyl] butanethioate
C25 H42 N7 O17 P3 S
CRFNGMNYKDXRTN-JSFVJHESSA-N
NDP
Query on NDP

Download Ideal Coordinates CCD File 
M [auth C]NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
NAP
Query on NAP

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
N [auth D]
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
2EC (Subject of Investigation/LOI)
Query on 2EC

Download Ideal Coordinates CCD File 
G [auth A],
J [auth B]
9-ETHYL-9H-PURIN-6-YLAMINE
C7 H9 N5
MUIPLRMGAXZWSQ-UHFFFAOYSA-N
VES
Query on VES

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
L [auth C],
P [auth D],
Q [auth D]
Pyrrolidine
C4 H9 N
RWRDLPDLKQPQOW-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.170 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.342α = 90
b = 78.829β = 108.06
c = 138.786γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2020-03-18 
  • Deposition Author(s): DeMirci, H.

Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesNSF-1231306

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-18
    Type: Initial release
  • Version 1.1: 2022-05-11
    Changes: Advisory, Database references
  • Version 1.2: 2024-05-22
    Changes: Data collection