5F1Q

Crystal Structure of Periplasmic Dipeptide Transport Protein from Yersinia pestis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal Structure of Periplasmic Dipeptide Transport Protein from Yersinia pestis

Kim, Y.Zhou, M.Shatsman, S.Anderson, W.F.Joachimiak, A.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Periplasmic dipeptide transport proteinA, B543Yersinia pestis Nepal516Mutation(s): 0 
Gene Names: YPN_3652
UniProt
Find proteins for A0A0H2YM47 (Yersinia pestis bv. Antiqua (strain Nepal516))
Explore A0A0H2YM47 
Go to UniProtKB:  A0A0H2YM47
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GLN
Query on GLN

Download Ideal Coordinates CCD File 
J [auth A], K [auth A], R [auth B], S [auth B]GLUTAMINE
C5 H10 N2 O3
ZDXPYRJPNDTMRX-VKHMYHEASA-N
 Ligand Interaction
PEG
Query on PEG

Download Ideal Coordinates CCD File 
F [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A] , E [auth A] , G [auth A] , I [auth A] , L [auth A] , M [auth B] , N [auth B] , P [auth B] , 
C [auth A],  E [auth A],  G [auth A],  I [auth A],  L [auth A],  M [auth B],  N [auth B],  P [auth B],  Q [auth B],  T [auth B],  U [auth B],  V [auth B],  W [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
H [auth A], O [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, BL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 289.29α = 90
b = 59.745β = 103.96
c = 80.631γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data scaling
HKL-3000phasing
SBC-Collectdata collection

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2015-12-23
    Type: Initial release
  • Version 1.1: 2019-11-27
    Changes: Author supporting evidence, Derived calculations