6WN8

2.70 Angstrom Resolution Crystal Structure of Uracil Phosphoribosyl Transferase from Klebsiella pneumoniae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.190 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history


Literature

A Structural Systems Biology Approach to High-Risk CG23 Klebsiella pneumoniae.

Inniss, N.L.Kochan, T.J.Minasov, G.Wawrzak, Z.Chang, C.Tan, K.Shuvalova, L.Kiryukhina, O.Pshenychnyi, S.Wu, R.Dubrovska, I.Babnigg, G.Endres, M.Anderson, W.F.Hauser, A.R.Joachimiak, A.Satchell, K.J.F.

(2023) Microbiol Resour Announc 12: e0101322-e0101322


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uracil phosphoribosyltransferase
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
211Klebsiella pneumoniae subsp. pneumoniaeMutation(s): 0 
Gene Names: 
EC: 2.4.2.9
UniProt
Find proteins for A6TCB0 (Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578))
Explore A6TCB0 
Go to UniProtKB:  A6TCB0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA6TCB0
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose
K
2N/A
Glycosylation Resources
GlyTouCan:  G05551OP
GlyCosmos:  G05551OP
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BDF
Query on BDF

Download Ideal Coordinates CCD File 
AA [auth B],
JB [auth E],
KB [auth E],
L [auth A],
M [auth A]
beta-D-fructopyranose
C6 H12 O6
LKDRXBCSQODPBY-ARQDHWQXSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AB [auth D]
AC [auth F]
AD [auth H]
BA [auth B]
BB [auth D]
AB [auth D],
AC [auth F],
AD [auth H],
BA [auth B],
BB [auth D],
BC [auth F],
BD [auth H],
CA [auth B],
CB [auth D],
CC [auth F],
CD [auth H],
DA [auth B],
DB [auth D],
DC [auth F],
DD [auth I],
EA [auth B],
EB [auth D],
ED [auth I],
FA [auth B],
FB [auth D],
FD [auth I],
GA [auth B],
GB [auth D],
GD [auth I],
HA [auth B],
HB [auth D],
HD [auth I],
IA [auth B],
IC [auth G],
ID [auth I],
JC [auth G],
JD [auth I],
KC [auth G],
KD [auth I],
LA [auth C],
LB [auth E],
LC [auth G],
LD [auth I],
MA [auth C],
MB [auth E],
MC [auth G],
N [auth A],
NA [auth C],
NB [auth E],
NC [auth G],
O [auth A],
OA [auth C],
OB [auth E],
OC [auth G],
OD [auth J],
P [auth A],
PA [auth C],
PB [auth E],
PC [auth G],
PD [auth J],
Q [auth A],
QA [auth C],
QB [auth E],
QD [auth J],
R [auth A],
RA [auth C],
RB [auth E],
RC [auth H],
RD [auth J],
S [auth A],
SA [auth C],
SC [auth H],
SD [auth J],
T [auth A],
TA [auth C],
TC [auth H],
TD [auth J],
U [auth A],
UA [auth C],
UC [auth H],
UD [auth J],
V [auth A],
VA [auth C],
VB [auth F],
VC [auth H],
WB [auth F],
WC [auth H],
XA [auth D],
XB [auth F],
XC [auth H],
YA [auth D],
YB [auth F],
YC [auth H],
ZA [auth D],
ZB [auth F],
ZC [auth H]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CL
Query on CL

Download Ideal Coordinates CCD File 
EC [auth F]
FC [auth F]
GC [auth F]
HC [auth F]
IB [auth D]
EC [auth F],
FC [auth F],
GC [auth F],
HC [auth F],
IB [auth D],
JA [auth B],
KA [auth B],
MD [auth I],
ND [auth I],
QC [auth G],
SB [auth E],
TB [auth E],
UB [auth E],
VD [auth J],
W [auth A],
WA [auth C],
WD [auth J],
X [auth A],
XD [auth J],
Y [auth A],
YD [auth J],
Z [auth A],
ZD [auth J]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.190 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 203.349α = 90
b = 203.349β = 90
c = 157.775γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-06
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2023-06-14
    Changes: Database references, Structure summary
  • Version 2.2: 2023-10-25
    Changes: Data collection, Refinement description