2D8W

Structure of HYPER-VIL-trypsin

Structural Biology Knowledgebase: 2D8W SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.256
  • R-Value Work: 0.222

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2D8W

Classification: HYDROLASE

Total Structure Weight: 24248.78

Macromolecule Entities
Molecule Chains Length Organism Details
Cationic trypsin A 223 Bos taurus EC#: 3.4.21.4 IUBMB
Mutation: Y48X, Y137X, Y171X
Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
IYR
Query on IYR
A L-PEPTIDE LINKING C9 H10 I N O3 TYR
TYI
Query on TYI
A L-PEPTIDE LINKING C9 H9 I2 N O3 TYR

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.256
  • R-Value Work: 0.222
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 54.32 α = 90.00
b = 58.20 β = 90.00
c = 66.62 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-12-08
  • Released Date: 2006-07-11
  • Deposition author(s): Miyatake, H., Hasegawa, T., Yamano, A.

Revision History

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