1Y4M

Crystal structure of human endogenous retrovirus HERV-FRD envelope protein (syncitin-2)

Structural Biology Knowledgebase: 1Y4M SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.262
  • R-Value Work: 0.248

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1Y4M

Classification: MEMBRANE PROTEIN

Total Structure Weight: 17404.72

Macromolecule Entities
Molecule Chains Length Organism Details
HERV-FRD_6p24.1 provirus ancestral Env polyprotein A, B, C 53 Homo sapiens Fragment: Ectodomain of the transmembrane subunit (residues 391-443).
Gene Name(s): ERVFRD-1 ERVFRDE1 UNQ6191/PRO20218

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
CL
Query on CL

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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.262
  • R-Value Work: 0.248
  • Space Group: I 4
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 90.40 α = 90.00
b = 90.40 β = 90.00
c = 38.65 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2004-12-01
  • Released Date: 2005-11-15
  • Deposition author(s): Renard, M., Varela, P.F., Letzelter, C., Duquerroy, S., Rey, F.A., Heidmann, T.

Revision History

  • 2011-11-16
    Type: Atom occupancy | Details: Atom occupancy
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4