2RCB

Crystal structure of the NR3B ligand binding core complex with D-serine at 1.62 Angstrom resolution

Structural Biology Knowledgebase: 2RCB SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.228
  • R-Value Work: 0.192

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2RCB

Classification: MEMBRANE PROTEIN

Total Structure Weight: 64664.00

Macromolecule Entities
Molecule Chains Length Organism Details
Glutamate [NMDA] receptor subunit 3B A, B 292 Rattus norvegicus Fragment: unp residues 413-560, 676-815
Gene Name(s): Grin3b

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

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

A 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 %)
DSN N/A in BindingDB
N/A in BindingMoad
Kd: 163 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.228
  • R-Value Work: 0.192
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 45.78 α = 90.00
b = 83.52 β = 90.00
c = 144.96 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