2QX0

Crystal Structure of Yersinia pestis HPPK (Ternary Complex)

Structural Biology Knowledgebase: 2QX0 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.269
  • R-Value Work: 0.230

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2QX0

Classification: TRANSFERASE

Total Structure Weight: 37513.95

Macromolecule Entities
Molecule Chains Length Organism Details
7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase A, B 159 Yersinia pestis EC#: 2.7.6.3 IUBMB
Gene Name(s): folK y0787 YP_0285 YPO3400

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
APC
Query on APC

A, B DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE (Synonym)
C11 H18 N5 O12 P3
CAWZRIXWFRFUQB-IOSLPCCCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PH2
Query on PH2

A, B 2-AMINO-6-HYDROXYMETHYL-7,8-DIHYDRO-3H-PTERIDIN- 4-ONE
C7 H9 N5 O2
CQQNNQTXUGLUEV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, B MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
PH2 N/A in BindingDB
Kd: 780 nM  BindingMOAD
Kd: 780 nM  PDBbind
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
CSO
Query on CSO
A, B L-PEPTIDE LINKING C3 H7 N O3 S CYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.269
  • R-Value Work: 0.230
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 43.40 α = 90.00
b = 78.62 β = 100.72
c = 52.60 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-08-10
  • Released Date: 2007-10-23
  • Deposition author(s): Blaszczyk, J., Cherry, S., Tropea, J.E., Waugh, D.S., Ji, X.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4