2VYX

Crystal structure of the T. thermophilus dodecin W38F mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Ultrafast Charge Transfer Dynamics in Flavoprotein Dodecin

Gurzadyan, G.G.Meissner, B.Sander, B.Essen, L.-O.Michel-Beyerle, M.E.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TTHA1431
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
69Thermus thermophilus HB8Mutation(s): 1 
UniProt
Find proteins for Q5SIE3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SIE3 
Go to UniProtKB:  Q5SIE3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SIE3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
COA
Query on COA

Download Ideal Coordinates CCD File 
AA [auth D]
DA [auth E]
FA [auth F]
IA [auth G]
LA [auth I]
AA [auth D],
DA [auth E],
FA [auth F],
IA [auth G],
LA [auth I],
MA [auth J],
N [auth A],
NA [auth K],
OA [auth L],
P [auth A],
S [auth B],
W [auth C]
COENZYME A
C21 H36 N7 O16 P3 S
RGJOEKWQDUBAIZ-IBOSZNHHSA-N
FMN
Query on FMN

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BA [auth D]
EA [auth F]
GA [auth F]
JA [auth H]
KA [auth H]
BA [auth D],
EA [auth F],
GA [auth F],
JA [auth H],
KA [auth H],
M [auth A],
O [auth A],
R [auth B],
T [auth B],
V [auth C],
X [auth C],
Z [auth D]
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
CA [auth D],
Q [auth A],
U [auth B],
Y [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
HA [auth F]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.63α = 90
b = 98.55β = 90
c = 139.84γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-11-17
    Type: Initial release
  • Version 1.1: 2011-05-07
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description