6UG4

Open Dimer of Y77A Mutant Putative Ryanodine Receptor from Bacteroides thetaiotaomicron VPI-5482


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Open Dimer of Y77A Mutant Putative Ryanodine Receptor from Bacteroides thetaiotaomicron VPI-5482

Wu, R.Jedrzejczak, R.Joachimiak, A.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative ryanodine receptor
A, B, C, D, E
A, B, C, D, E, F
100Bacteroides thetaiotaomicron VPI-5482Mutation(s): 1 
Gene Names: BT_2247
UniProt
Find proteins for Q8A5J2 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50))
Explore Q8A5J2 
Go to UniProtKB:  Q8A5J2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8A5J2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CFF (Subject of Investigation/LOI)
Query on CFF

Download Ideal Coordinates CCD File 
AA [auth F]
BA [auth F]
G [auth A]
H [auth A]
I [auth A]
AA [auth F],
BA [auth F],
G [auth A],
H [auth A],
I [auth A],
O [auth C],
P [auth C],
Q [auth C],
W [auth E]
CAFFEINE
C8 H10 N4 O2
RYYVLZVUVIJVGH-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
K [auth A],
L [auth A],
N [auth B],
T [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
CA [auth F]
DA [auth F]
EA [auth F]
J [auth A]
M [auth B]
CA [auth F],
DA [auth F],
EA [auth F],
J [auth A],
M [auth B],
R [auth C],
S [auth C],
X [auth E],
Y [auth E],
Z [auth E]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
PYR
Query on PYR

Download Ideal Coordinates CCD File 
U [auth D],
V [auth D]
PYRUVIC ACID
C3 H4 O3
LCTONWCANYUPML-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E
A, B, C, D, E, F
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.201α = 90
b = 84.201β = 90
c = 229.704γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000phasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-05
    Type: Initial release
  • Version 2.0: 2023-11-15
    Changes: Advisory, Atomic model, Data collection, Database references
  • Version 2.1: 2024-10-23
    Changes: Structure summary