4H1T

X-RAY Structure of the Complex VchUPh with Phosphate ion at 1.92A Resolution.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

X-RAY Structure of the Complex VchUPh with Phosphate ion at 1.92A Resolution.

Prokofev, I.I.Lashkov, A.A.Gabdoulkhakov, A.G.Sotnichenko, S.E.Betzel, C.Mikhailov, A.M.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uridine phosphorylase
A, B, C, D, E
A, B, C, D, E, F
253Vibrio choleraeMutation(s): 0 
Gene Names: udp
EC: 2.4.2.3
UniProt
Find proteins for Q9K4U1 (Vibrio cholerae)
Explore Q9K4U1 
Go to UniProtKB:  Q9K4U1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9K4U1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PEG
Query on PEG

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AA [auth A]
AC [auth E]
BA [auth A]
BC [auth E]
CA [auth A]
AA [auth A],
AC [auth E],
BA [auth A],
BC [auth E],
CA [auth A],
CC [auth E],
DA [auth A],
EA [auth A],
EB [auth C],
FA [auth A],
FB [auth C],
GB [auth C],
HB [auth C],
IB [auth C],
JB [auth C],
OC [auth F],
PC [auth F],
QA [auth B],
QB [auth D],
QC [auth F],
RA [auth B],
RB [auth D],
RC [auth F],
SA [auth B],
SC [auth F],
TC [auth F],
UC [auth F],
Z [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4
Query on SO4

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FC [auth F]
IA [auth B]
JA [auth B]
KB [auth D]
TB [auth E]
FC [auth F],
IA [auth B],
JA [auth B],
KB [auth D],
TB [auth E],
UB [auth E],
WA [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
PO4
Query on PO4

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DC [auth F],
GA [auth B],
HA [auth B],
TA [auth C]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO
Query on EDO

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AB [auth C]
BB [auth C]
CB [auth C]
GC [auth F]
H [auth A]
AB [auth C],
BB [auth C],
CB [auth C],
GC [auth F],
H [auth A],
HC [auth F],
I [auth A],
IC [auth F],
J [auth A],
JC [auth F],
K [auth A],
KA [auth B],
KC [auth F],
L [auth A],
LA [auth B],
LB [auth D],
LC [auth F],
M [auth A],
MA [auth B],
MB [auth D],
MC [auth F],
N [auth A],
NB [auth D],
O [auth A],
OA [auth B],
OB [auth D],
P [auth A],
PA [auth B],
Q [auth A],
S [auth A],
T [auth A],
U [auth A],
V [auth A],
VB [auth E],
W [auth A],
WB [auth E],
X [auth A],
XA [auth C],
XB [auth E],
YA [auth C],
YB [auth E],
ZA [auth C],
ZB [auth E]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
EOH
Query on EOH

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DB [auth C]
NA [auth B]
NC [auth F]
PB [auth D]
R [auth A]
DB [auth C],
NA [auth B],
NC [auth F],
PB [auth D],
R [auth A],
Y [auth A]
ETHANOL
C2 H6 O
LFQSCWFLJHTTHZ-UHFFFAOYSA-N
K
Query on K

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UA [auth C]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL
Query on CL

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EC [auth F],
VA [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

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G [auth A],
SB [auth E]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.691α = 69.62
b = 71.08β = 72.56
c = 87.937γ = 85.74
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-09-11
    Type: Initial release
  • Version 1.1: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description