4B0P

Crystal structure of soman-aged human butyrylcholinesterase in complex with methyl 2-(pentafluorobenzyloxyimino)pyridinium

Structural Biology Knowledgebase: 4B0P SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.212
  • R-Value Work: 0.164

Literature

Macromolecules
Sequence Display for 4B0P

Classification: HYDROLASE

Total Structure Weight: 62597.64

Macromolecule Entities
Molecule Chains Length Organism Details
CHOLINESTERASE A 529 Homo sapiens EC#: 3.1.1.8 IUBMB
Fragment: RESIDUES 29-557
Mutation: N17Q, N384Q, N455Q, N481Q
Gene Name(s): BCHE Gene View CHE1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 8 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
MF5
Query on MF5

A 1-(1-methylpyridin-1-ium-2-yl)-N-[[2,3,4,5,6- pentakis(fluoranyl)phenyl]methoxy]methanimine
methyl2-(pentafluorobenzyloxyimino)pyridinium (Synonym)
C14 H10 F5 N2 O
HYLZTSPDSFFOSU-CGOBSMCZSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

A N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FUL
Query on FUL

A BETA-L-FUCOSE
6-DEOXY-BETA-L-GALACTOSE (Synonym)
C6 H12 O5
SHZGCJCMOBCMKK-KGJVWPDLSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GLY
Query on GLY

A GLYCINE
C2 H5 N O2
DHMQDGOQFOQNFH-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)
K
Query on K

A POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
MF5 N/A in BindingDB
Ki: 44000 nM  BindingMOAD
N/A in PDBbind
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
SBG
Query on SBG
A NON-POLYMER C4 H10 N O5 P SER

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.212
  • R-Value Work: 0.164
  • Space Group: I 4 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 154.23 α = 90.00
b = 154.23 β = 90.00
c = 133.86 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-07-04
  • Released Date: 2012-08-29
  • Deposition author(s): Wandhammer, M., de Koning, M., van Grol, M., Noort, D., Goeldner, M., Nachon, F.

Revision History

  • 2013-04-17
    Type: Citation | Details: JRNL
  • 2012-10-17
    Type: Citation | Details: JRNL