1RQD

deoxyhypusine synthase holoenzyme in its low ionic strength, high pH crystal form with the inhibitor GC7 bound in the active site

Structural Biology Knowledgebase: 1RQD SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0 Å
  • R-Value Free: 0.232
  • R-Value Work: 0.196

Literature

Macromolecules
Sequence Display for 1RQD

Classification: Transferase

Total Structure Weight: 83701.10

Macromolecule Entities
Molecule Chains Length Organism Details
Deoxyhypusine synthase A, B 369 Homo sapiens EC#: 2.5.1.46 IUBMB
Gene Name(s): DHPS Gene View DS
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GC7
Query on GC7

A, B 1-GUANIDINIUM-7-AMINOHEPTANE
C8 H22 N4
SKGAVCHIFDRDTK-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
GC7 IC50: 30 nM (92) BindingDB

N/A in BindingMoad
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0 Å
  • R-Value Free: 0.232
  • R-Value Work: 0.196
  • Space Group: P 32 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 104.78 α = 90.00
b = 104.78 β = 90.00
c = 159.25 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-12-04
  • Released Date: 2004-07-13
  • Deposition author(s): Umland, T.C., Wolff, E.C., Park, M.-H., Davies, D.R.

Revision History

  • 2014-11-12
    Type: Function and keywords | Details: --
  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4