3RSR

Crystal Structure of 5-NITP Inhibition of Yeast Ribonucleotide Reductase

Structural Biology Knowledgebase: 3RSR SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.233
  • R-Value Work: 0.188

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3RSR

Classification: OXIDOREDUCTASE

Total Structure Weight: 100216.21

Macromolecule Entities
Molecule Chains Length Organism Details
Ribonucleoside-diphosphate reductase large chain 1 A 888 Saccharomyces cerevisiae EC#: 1.17.4.1 IUBMB
Gene Name(s): RNR1 CRT7 RIR1 SDS12 YER070W

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

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
N5P
Query on N5P

A 1-{2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}PHOSPHORYL]- BETA-D-ERYTHRO-PENTOFURANOSYL}-5-NITRO-1H- INDOLE
5-NITRO-1-INDOLYL-2'-DEOXYRIBOSIDE-5'-TRIPHOSPHATE (Synonym)
C13 H17 N2 O14 P3
JJJBDAFRCKSXDR-YNEHKIRRSA-N
Ligand Explorer
 
JSmol
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
N5P N/A in BindingDB
Kd: 44000 nM  BindingMOAD
Kd: 44000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.233
  • R-Value Work: 0.188
  • Space Group: P 21 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 108.35 α = 90.00
b = 118.21 β = 90.00
c = 63.92 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-05-02
  • Released Date: 2012-11-14
  • Deposition author(s): Wan, Q., Mohammed, F., Jha, S., Motea, E., Berdis, A., Dealwis, C.G.

Revision History

No revisions since initial release