5HI6

The high resolution structure of dihydrofolate reductase from Yersinia pestis complex with methotrexate as closed form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.051 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The high resolution structure of dihydrofolate reductase from Yersinia pestis complex with methotrexate as closed form

Chang, C.Maltseva, N.Kim, Y.Makowska-Grzyska, M.Mulligan, R.Papazisi, L.Anderson, W.F.Joachimiak, A.Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dihydrofolate reductase
A, B
163Yersinia pestisMutation(s): 0 
Gene Names: folA
EC: 1.5.1.3
Find proteins for A0A384KYY5 (Yersinia pestis)
Go to UniProtKB:  A0A384KYY5
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

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Download CCD File 
A, B
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MTX
Query on MTX

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Download CCD File 
A, B
METHOTREXATE
C20 H22 N8 O5
FBOZXECLQNJBKD-ZDUSSCGKSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 44.151α = 90.00
b = 60.623β = 90.00
c = 109.942γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
Cootmodel building
BUCCANEERmodel building
MOLREPphasing
SCALEPACKdata scaling
HKL-3000phasing
HKL-3000data reduction
PHENIXrefinement
SBC-Collectdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-02-03
    Type: Initial release
  • Version 1.1: 2016-02-10
    Type: Database references, Structure summary
  • Version 1.2: 2017-11-22
    Type: Derived calculations, Refinement description