1ZHN

Crystal Structure of mouse CD1d bound to the self ligand phosphatidylcholine

Structural Biology Knowledgebase: 1ZHN SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.281
  • R-Value Work: 0.216

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1ZHN

Classification: IMMUNE SYSTEM MEMBRANE PROTEIN

Total Structure Weight: 45377.59

Macromolecule Entities
Molecule Chains Length Organism Details
CD1d1 antigen A 273 Mus musculus Details: Self phospholipid copurified with protein
Gene Name(s): Cd1d1 Cd1.1
beta-2-microglobulin B 99 Mus musculus Gene Name(s): B2m

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
PC6
Query on PC6

A 7-[(DODECANOYLOXY)METHYL]-4-HYDROXY-N,N,N- TRIMETHYL-9-OXO-3,5,8-TRIOXA-4-PHOSPHADOTRIACONTAN- 1-AMINIUM 4-OXIDE
C45 H90 N O8 P
KWHAREAUZBVBDS-VZUYHUTRSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

A N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MAN
Query on MAN

A ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FUC
Query on FUC

A ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.281
  • R-Value Work: 0.216
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 41.80 α = 90.00
b = 106.91 β = 90.00
c = 110.06 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-04-26
  • Released Date: 2005-07-19
  • Deposition author(s): Giabbai, B., Sidobre, S., Crispin, M.M.D., Sanchez Ruiz, Y., Bachi, A., Kronenberg, M., Wilson, I.A., Degano, M.

Revision History

  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4