4AB9

Fragments bound to bovine trypsin for the SAMPL challenge

Structural Biology Knowledgebase: 4AB9 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.162
  • R-Value Work: 0.140

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4AB9

Classification: HYDROLASE

Total Structure Weight: 23874.06

Macromolecule Entities
Molecule Chains Length Organism Details
CATIONIC TRYPSIN A 223 Bos taurus EC#: 3.4.21.4 IUBMB
Details: PROTEASE
Gene Name(s):

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
VXQ
Query on VXQ

A 1-(2,3-dihydro-1-benzofuran-5-yl)methanamine
C9 H11 N O
WQXWNTPLZFVZNX-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)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
VXQ N/A in BindingDB
N/A in BindingMoad
Kd: 466000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.162
  • R-Value Work: 0.140
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 54.75 α = 90.00
b = 58.50 β = 90.00
c = 66.99 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