2RC8

Crystal structure of the NR3A ligand binding core complex with D-serine at 1.45 Angstrom resolution

Structural Biology Knowledgebase: 2RC8 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.178
  • R-Value Work: 0.153

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2RC8

Classification: MEMBRANE PROTEIN

Total Structure Weight: 66360.82

Macromolecule Entities
Molecule Chains Length Organism Details
Glutamate [NMDA] receptor subunit 3A A, B 294 Rattus norvegicus Fragment: unp residues 511-660, 776-915
Gene Name(s): Grin3a

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

A D-SERINE
C3 H7 N O3
MTCFGRXMJLQNBG-UWTATZPHSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A, B GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A, B CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
DSN N/A in BindingDB
N/A in BindingMoad
IC50: 300 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.178
  • R-Value Work: 0.153
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 49.79 α = 90.00
b = 97.70 β = 93.60
c = 60.05 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-09-19
  • Released Date: 2008-08-05
  • Deposition author(s): Yao, Y., Mayer, M.L.

Revision History

  • 2011-07-13
    Type: Flag residual B-value | Details: Tagged residual B temperature factor
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4