1DET

RIBONUCLEASE T1 CARBOXYMETHYLATED AT GLU 58 IN COMPLEX WITH 2'GMP

Structural Biology Knowledgebase: 1DET SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Observed: 0.194

Literature

Macromolecules
Sequence Display for 1DET

Classification: HYDROLASE (ENDORIBONUCLEASE)

Total Structure Weight: 11560.97

Macromolecule Entities
Molecule Chains Length Organism Details
RIBONUCLEASE T1 A 104 Aspergillus oryzae EC#: 3.1.27.3 IUBMB
Details: THE G-CARBOXYL GROUP OF GLU 58 IS CARBOXYMETHYLATED
Gene Name(s): rntA AO090011000118
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A GUANOSINE-2'-MONOPHOSPHATE
C10 H14 N5 O8 P
WTIFIAZWCCBCGE-UUOKFMHZSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
2GP N/A in BindingDB
Kd: 50000 nM  BindingMOAD
Kd: 50000 nM  PDBbind
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
CGA
Query on CGA
A L-PEPTIDE LINKING C7 H11 N O6 GLU

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Observed: 0.194
  • Space Group: I 2 3
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 88.69 α = 90.00
b = 88.69 β = 90.00
c = 88.69 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1996-02-20
  • Released Date: 1996-07-11
  • Deposition author(s): Ishikawa, K., Suzuki, E., Tanokura, M., Takahashi, K.

Revision History

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