1WDY

Crystal structure of ribonuclease

Structural Biology Knowledgebase: 1WDY SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.230
  • R-Value Work: 0.202

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1WDY

Classification: Hydrolase

Total Structure Weight: 32182.64

Macromolecule Entities
Molecule Chains Length Organism Details
2-5A-dependent ribonuclease A 285 Homo sapiens EC#: 3.1.26 IUBMB
Fragment: residues 21-305
Mutation: I97L
Gene Name(s): RNASEL Gene View RNS4

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
25A
Query on 25A

A 5'-O-MONOPHOSPHORYLADENYLYL(2'->5')ADENYLYL(2'- >5')ADENOSINE
C30 H38 N15 O19 P3
SIIZPVYVXNXXQG-UQTMIEBXSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
25A EC50: 0.15 - 0.21 nM (99) BindingDB
IC50: 1.1 - 20 nM (99) BindingDB

N/A in BindingMoad
IC50: 13 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.230
  • R-Value Work: 0.202
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 63.20 α = 90.00
b = 72.83 β = 90.00
c = 82.63 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2004-05-19
  • Released Date: 2004-10-05
  • Deposition author(s): Tanaka, N., Nakanishi, M., Kusakabe, Y., Goto, Y., Kitade, Y., Nakamura, K.T.

Revision History

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