3IEL

Crystal Structure of TTHA0252 from Thermus thermophilus HB8 complexed with UMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.222 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Crystal Structure of TTHA0252 from Thermus thermophilus HB8 complexed with UMP

Ishikawa, H.Nakagawa, N.Kuramitsu, S.Masui, R.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribonuclease TTHA0252
A, B, C, D
431Thermus thermophilus HB8Mutation(s): 0 
Gene Names: TTHA0252
EC: 3.1
UniProt
Find proteins for Q5SLP1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SLP1 
Go to UniProtKB:  Q5SLP1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SLP1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
U5P
Query on U5P

Download Ideal Coordinates CCD File 
KD [auth D]
LA [auth A]
MA [auth A]
NA [auth A]
OB [auth B]
KD [auth D],
LA [auth A],
MA [auth A],
NA [auth A],
OB [auth B],
PB [auth B],
RC [auth C]
URIDINE-5'-MONOPHOSPHATE
C9 H13 N2 O9 P
DJJCXFVJDGTHFX-XVFCMESISA-N
FLC
Query on FLC

Download Ideal Coordinates CCD File 
KA [auth A],
NB [auth B]
CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth A]
AB [auth B]
AC [auth C]
AD [auth D]
BA [auth A]
AA [auth A],
AB [auth B],
AC [auth C],
AD [auth D],
BA [auth A],
BB [auth B],
BC [auth C],
BD [auth D],
CA [auth A],
CB [auth B],
CC [auth C],
CD [auth D],
DA [auth A],
DB [auth B],
DC [auth C],
DD [auth D],
E [auth A],
EA [auth A],
EB [auth B],
EC [auth C],
ED [auth D],
F [auth A],
FA [auth A],
FB [auth B],
FC [auth C],
FD [auth D],
G [auth A],
GA [auth A],
GB [auth B],
GC [auth C],
GD [auth D],
H [auth A],
HA [auth A],
HB [auth B],
HC [auth C],
HD [auth D],
I [auth A],
IA [auth A],
IB [auth B],
IC [auth C],
ID [auth D],
J [auth A],
JA [auth A],
JB [auth B],
JC [auth C],
JD [auth D],
K [auth A],
KB [auth B],
KC [auth C],
L [auth A],
LB [auth B],
LC [auth C],
M [auth A],
MB [auth B],
MC [auth C],
N [auth A],
NC [auth C],
O [auth A],
OC [auth C],
P [auth A],
PC [auth C],
Q [auth A],
QA [auth B],
QC [auth C],
R [auth A],
RA [auth B],
S [auth A],
SA [auth B],
SB [auth C],
T [auth A],
TA [auth B],
TB [auth C],
U [auth A],
UA [auth B],
UB [auth C],
UC [auth D],
V [auth A],
VA [auth B],
VB [auth C],
VC [auth D],
W [auth A],
WA [auth B],
WB [auth C],
WC [auth D],
X [auth A],
XA [auth B],
XB [auth C],
XC [auth D],
Y [auth A],
YA [auth B],
YB [auth C],
YC [auth D],
Z [auth A],
ZA [auth B],
ZB [auth C],
ZC [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ZN
Query on ZN

Download Ideal Coordinates CCD File 
LD [auth D]
MD [auth D]
OA [auth A]
PA [auth A]
QB [auth B]
LD [auth D],
MD [auth D],
OA [auth A],
PA [auth A],
QB [auth B],
RB [auth B],
SC [auth C],
TC [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.222 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 145.238α = 90
b = 146.677β = 110.11
c = 120.349γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
XFITdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-07-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description