2YME

Crystal structure of a mutant binding protein (5HTBP-AChBP) in complex with granisetron

Structural Biology Knowledgebase: 2YME SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.226
  • R-Value Work: 0.169

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2YME

Classification: RECEPTOR

Total Structure Weight: 239045.89

Macromolecule Entities
Molecule Chains Length Organism Details
SOLUBLE ACETYLCHOLINE RECEPTOR A, B, C..., D, E, F, G, H, I, JA, B, C, D, E, F, G, H, I, J 205 Aplysia californica Fragment: ACETYLCHOLINE BINDING DOMAIN, RESIDUES 20-224
Mutation: A41V, Y53W, Q55R, A136V
Gene Name(s):

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

A, B, C, D, E, F, G, H, I, J 1-methyl-N-[(1R,5S)-9-methyl-9-azabicyclo[3.3.1]nonan- 3-yl]indazole-3-carboxamide
GRANISETRON (Synonym)
C18 H24 N4 O
MFWNKCLOYSRHCJ-BTTYYORXSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

A, B, C, D, E, F, H, I, J N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO4
Query on PO4

A, C, E, G, H PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

I SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
CWB N/A in BindingDB
Kd: 549 nM  BindingMOAD
Kd: 22 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.226
  • R-Value Work: 0.169
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 83.09 α = 90.00
b = 138.90 β = 91.07
c = 119.89 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-10-09
  • Released Date: 2012-12-26
  • Deposition author(s): Kesters, D., Thompson, A.J., Brams, M., Elk, R.V., Spurny, R., Geitmann, M., Villalgordo, J.M., Guskov, A., Danielson, U.H., Lummis, S.C.R., Smit, A.B., Ulens, C.

Revision History

  • 2013-01-30
    Type: Citation | Details: JRNL