2J9N

Robotically harvested Trypsin complexed with Benzamidine containing polypeptide mediated crystal contacts

Structural Biology Knowledgebase: 2J9N SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.176
  • R-Value Work: 0.154

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2J9N

Classification: HYDROLASE

Total Structure Weight: 25212.69

Macromolecule Entities
Molecule Chains Length Organism Details
CATIONIC TRYPSIN A 223 Bos taurus EC#: 3.4.21.4 IUBMB
Fragment: RESIDUES 21-243
Gene Name(s):
UNKNOWN PEPTIDE B 15 synthetic
UNKNOWN PEPTIDE C 3 synthetic

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
BEN
Query on BEN

A BENZAMIDINE
C7 H8 N2
PXXJHWLDUBFPOL-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
IPH
Query on IPH

A PHENOL
C6 H6 O
ISWSIDIOOBJBQZ-UHFFFAOYSA-N
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)
NA
Query on NA

A SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
BEN Ki: 31 - 39000 nM (100) BindingDB

N/A in BindingMoad
Kd: 20000 nM  PDBbind
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
UNK
Query on UNK
B, C L-PEPTIDE LINKING C4 H9 N O2 --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.176
  • R-Value Work: 0.154
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 53.92 α = 90.00
b = 56.69 β = 90.00
c = 66.05 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2006-11-14
  • Released Date: 2007-04-03
  • Deposition author(s): Viola, R., Carman, P., Walsh, J., Miller, E., Benning, M., Frankel, D., McPherson, A., Cudney, R., Rupp, B.

Revision History

  • 2012-06-20
    Type: Refinement description | Details: REMARK 3
  • 2012-06-20
    Type: Non-polymer description | Details: FORMUL
  • 2012-06-20
    Type: Other | Details: REMARK 525,REMARK 900
  • 2012-06-20
    Type: Version format compliance | Details: REMARK 4
  • 2012-06-20
    Type: Citation | Details: JRNL
  • 2012-06-20
    Type: Biological assembly | Details: REMARK 300,REMARK 350
  • 2012-06-20
    Type: Geometry validation | Details: REMARK 500