3V13

Bovine trypsin variant X(tripleGlu217Phe227) in complex with small molecule inhibitor

Structural Biology Knowledgebase: 3V13 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.175
  • R-Value Work: 0.146

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3V13

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 24466.98

Macromolecule Entities
Molecule Chains Length Organism Details
Cationic trypsin A 223 Bos taurus EC#: 3.4.21.4 IUBMB
Mutation: N97E, L99Y, Y172S, P173S, G174F, Q175I, A183V, S190A, S217E, V227F
Gene Name(s):

Small Molecules
Ligands 6 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
3YH
Query on 3YH

A 3-(3-carbamimidoylphenyl)-N-(2'-sulfamoylbiphenyl- 4-yl)-1,2-oxazole-4-carboxamide
C23 H19 N5 O4 S
LPYBKEFBMJIVEB-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
IMD
Query on IMD

A IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
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)
CL
Query on CL

A CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
3YH Ki: 21 nM (95) BindingDB

N/A in BindingMoad
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.175
  • R-Value Work: 0.146
  • Space Group: P 65
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 81.81 α = 90.00
b = 81.81 β = 90.00
c = 63.87 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-12-09
  • Released Date: 2012-12-12
  • Deposition author(s): Tziridis, A., Neumann, P., Kolenko, P., Stubbs, M.T.

Revision History

  • 2014-07-16
    Type: Citation | Details: Citation update