4AB8

Fragments bound to bovine trypsin for the SAMPL challenge

Structural Biology Knowledgebase: 4AB8 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.205
  • R-Value Work: 0.169

Literature

Macromolecules
Sequence Display for 4AB8

Classification: HYDROLASE

Total Structure Weight: 23950.10

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

Membrane Protein

Source: inferred by homology | Group: BETA-BARREL

Subgroup Name: Omp85-TpsB Outer Membrane Transporter Superfamily

Protein Name: BamABCDE complex of the Bam β-barrel assembly machine


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

A 3,4-dihydro-2H-1,5-benzodioxepin-6-ylmethanamine
CC00413 (Synonym)
C10 H13 N O2
ZXJOKQNPRXXPJT-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

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

A CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
VXU N/A in BindingDB
N/A in BindingMoad
Kd: 136000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.205
  • R-Value Work: 0.169
  • Space Group: P 31 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 54.32 α = 90.00
b = 54.32 β = 90.00
c = 105.32 γ = 120.00

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