6III

Crystal structure of an uncharacterized protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Crystal structure of an uncharacterized protein

Li, B.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
UPF0061 protein YdiUA482Escherichia coliMutation(s): 0 
Gene Names: ydiUBMT91_02235NCTC9073_05692PGD_01529SAMEA3472078_00997SAMEA3484419_01283SAMEA3752562_01353SAMEA3753069_03695SAMEA3753077_01245
EC: 2.7.7
UniProt
Find proteins for P77649 (Escherichia coli (strain K12))
Explore P77649 
Go to UniProtKB:  P77649
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP77649
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AMP
Query on AMP

Download Ideal Coordinates CCD File 
C [auth A]ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
2PN
Query on 2PN

Download Ideal Coordinates CCD File 
B [auth A]IMIDODIPHOSPHORIC ACID
H5 N O6 P2
GNGSOPFGGKKDQP-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.208 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.424α = 90
b = 71.424β = 90
c = 363.446γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

  • Deposited Date: 2018-10-06 
  • Released Date: 2019-10-09 
  • Deposition Author(s): Li, B., Yuan, Z.

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-09
    Type: Initial release