2TIO

LOW PACKING DENSITY FORM OF BOVINE BETA-TRYPSIN IN CYCLOHEXANE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

X-ray studies on two forms of bovine beta-trypsin crystals in neat cyclohexane.

Zhu, G.Huang, Q.Wang, Z.Qian, M.Jia, Y.Tang, Y.

(1998) Biochim.Biophys.Acta 1429: 142-150

  • Primary Citation of Related Structures:  1TIO

  • PubMed Abstract: 
  • Two orthorhombic forms (Vm values are 2.3 and 3.0 A3/Da) of bovine beta-trypsin crystals in neat cyclohexane were determined to 1.93 A resolution, by X-ray diffraction. Both structures in organic solvent are similar to those in aqueous solution. In t ...

    Two orthorhombic forms (Vm values are 2.3 and 3.0 A3/Da) of bovine beta-trypsin crystals in neat cyclohexane were determined to 1.93 A resolution, by X-ray diffraction. Both structures in organic solvent are similar to those in aqueous solution. In the high packing density form, one cyclohexane molecule is found in a hydrophobic site near the active center. One sulfate locates at the active site with hydrogen or salt bond to the Ser-His catalytic diad, and five more sulfates bind on the molecular surface. The conformation of the side chains near the sulfates changed greatly. In the low packing density form, one cyclohexane and three sulfates are found. In both structures, one benzamidine molecule locates at the hydrophobic pocket of the active center. Most water molecules on the enzyme surface are retained except some with high temperature factors.


    Organizational Affiliation

    Department of Chemistry, Peking University, Beijing, PR China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (BETA-TRYPSIN)
A
223Bos taurusEC: 3.4.21.4
Find proteins for P00760 (Bos taurus)
Go to UniProtKB:  P00760
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
HEX
Query on HEX

Download SDF File 
Download CCD File 
A
HEXANE
C6 H14
VLKZOEOYAKHREP-UHFFFAOYSA-N
 Ligand Interaction
BEN
Query on BEN

Download SDF File 
Download CCD File 
A
BENZAMIDINE
C7 H8 N2
PXXJHWLDUBFPOL-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BDNKi: 31 - 39000 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.179 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 63.020α = 90.00
b = 63.780β = 90.00
c = 69.040γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-09-30
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance