4ABE

Fragments bound to bovine trypsin for the SAMPL challenge

Structural Biology Knowledgebase: 4ABE SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.171
  • R-Value Work: 0.150

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4ABE

Classification: HYDROLASE

Total Structure Weight: 24153.74

Macromolecule Entities
Molecule Chains Length Organism Details
CATIONIC TRYPSIN A 223 Bos taurus EC#: 3.4.21.4 IUBMB
Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 6 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
913
Query on 913

A (3-PYRAZOL-1-YLPHENYL)METHANAMINE
FRAGMENT CC32913 (Synonym)
C10 H11 N3
YWZKZHCZKIKAAC-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)
DMS
Query on DMS

A DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

A 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-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)
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 %)
913 N/A in BindingDB
N/A in BindingMoad
Kd: 400000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.171
  • R-Value Work: 0.150
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 54.37 α = 90.00
b = 58.65 β = 90.00
c = 66.45 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-12-08
  • Released Date: 2012-02-08
  • Deposition author(s): Newman, J., Peat, T.S.

Revision History

  • 2014-02-05
    Type: Citation | Details: REMARK 1, JRNL