6LRT

Crystal structure of isocitrate lyase (Caur_3889) from Chloroflexus aurantiacus in complex with isocitrate and manganese ion


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structural studies reveal the molecular mechanism of isocitrate lyase from Chloroflexus aurantiacus

Lee, S.H.Kim, K.J.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Isocitrate lyase436Chloroflexus aurantiacus J-10-flMutation(s): 0 
Gene Names: Caur_3889
UniProt
Find proteins for A9WDE7 (Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))
Explore A9WDE7 
Go to UniProtKB:  A9WDE7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA9WDE7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ICT (Subject of Investigation/LOI)
Query on ICT

Download Ideal Coordinates CCD File 
BA [auth S]
GA [auth V]
I [auth A]
L [auth D]
O [auth G]
BA [auth S],
GA [auth V],
I [auth A],
L [auth D],
O [auth G],
S [auth J],
W [auth M],
Y [auth P]
ISOCITRIC ACID
C6 H8 O7
ODBLHEXUDAPZAU-ZAFYKAAXSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
CA [auth S]
DA [auth S]
EA [auth S]
HA [auth V]
IA [auth V]
CA [auth S],
DA [auth S],
EA [auth S],
HA [auth V],
IA [auth V],
J [auth A],
M [auth D],
P [auth G],
Q [auth G],
T [auth J],
U [auth J],
Z [auth P]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MN (Subject of Investigation/LOI)
Query on MN

Download Ideal Coordinates CCD File 
AA [auth P]
FA [auth S]
JA [auth V]
K [auth A]
N [auth D]
AA [auth P],
FA [auth S],
JA [auth V],
K [auth A],
N [auth D],
R [auth G],
V [auth J],
X [auth M]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.179 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 157.314α = 90
b = 157.314β = 90
c = 197.707γ = 120
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-28
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Database references, Refinement description