4M8L

crystal structure of RpiA-R5P complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.239 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribose-5-phosphate isomerase A
A, B, C, D
224Francisella tularensisMutation(s): 0 
Gene Names: rpiAFTW_1255
EC: 5.3.1.6
UniProt
Find proteins for A4IYN5 (Francisella tularensis subsp. tularensis (strain WY96-3418))
Explore A4IYN5 
Go to UniProtKB:  A4IYN5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA4IYN5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
5RP
Query on 5RP

Download Ideal Coordinates CCD File 
E [auth A],
MA [auth C],
V [auth B],
ZA [auth D]
RIBULOSE-5-PHOSPHATE
C5 H11 O8 P
FNZLKVNUWIIPSJ-UHNVWZDZSA-N
ARF
Query on ARF

Download Ideal Coordinates CCD File 
AA [auth B]
AB [auth D]
BA [auth B]
BB [auth D]
CA [auth B]
AA [auth B],
AB [auth D],
BA [auth B],
BB [auth D],
CA [auth B],
DA [auth B],
EA [auth B],
F [auth A],
FA [auth B],
G [auth A],
GA [auth B],
H [auth A],
HA [auth B],
I [auth A],
IA [auth B],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
NA [auth C],
O [auth A],
OA [auth C],
P [auth A],
PA [auth C],
Q [auth A],
QA [auth C],
R [auth A],
RA [auth C],
S [auth A],
SA [auth C],
T [auth A],
TA [auth C],
UA [auth C],
VA [auth C],
W [auth B],
WA [auth C],
X [auth B],
XA [auth C],
Y [auth B],
Z [auth B]
FORMAMIDE
C H3 N O
ZHNUHDYFZUAESO-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
JA [auth B],
KA [auth B],
LA [auth B],
U [auth A],
YA [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.239 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 168.203α = 90
b = 151.958β = 93.98
c = 36.29γ = 90
Software Package:
Software NamePurpose
HKL-3000data collection
MOLREPphasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-02
    Type: Initial release
  • Version 1.1: 2013-10-09
    Changes: Other
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description