2YMD

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

Structural Biology Knowledgebase: 2YMD SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.201
  • R-Value Work: 0.159

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2YMD

Classification: RECEPTOR

Total Structure Weight: 244932.21

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 212 Aplysia californica Fragment: ACETYLCHOLINE BINDING DOMAIN, RESIDUES 20-231
Mutation: A41V, Y53W, S92E, A136V, V140L, K141T
Gene Name(s):

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

A, B, C, D, E, F, G, H, I, J SEROTONIN
3-(2-AMINOETHYL)-1H-INDOL-5-OL (Synonym)
C10 H12 N2 O
QZAYGJVTTNCVMB-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO4
Query on PO4

A, B, C, D, E, F, G, H, I, J PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A, B, C, D, E, F, G, J GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
SRO N/A in BindingDB
Kd: 693000 nM  BindingMOAD
Kd: 693000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.201
  • R-Value Work: 0.159
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 203.57 α = 90.00
b = 140.06 β = 99.08
c = 126.53 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-10-09
  • Released Date: 2012-12-12
  • 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