1ZT4

The crystal structure of human CD1d with and without alpha-Galactosylceramide

Structural Biology Knowledgebase: 1ZT4 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0 Å
  • R-Value Free: 0.326
  • R-Value Work: 0.234

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1ZT4

Classification: IMMUNE SYSTEM

Total Structure Weight: 88255.53

Macromolecule Entities
Molecule Chains Length Organism Details
T-cell surface glycoprotein CD1d A, C 281 Homo sapiens Fragment: CD1d heavy chain
Gene Name(s): CD1D Gene View
Beta-2-microglobulin B, D 100 Homo sapiens Gene Name(s): B2M Gene View CDABP0092 HDCMA22P

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

A N-{(1S,2R,3S)-1-[(ALPHA-D-GALACTOPYRANOSYLOXY)METHYL]- 2,3-DIHYDROXYHEPTADECYL}HEXACOSANAMIDE
C50 H99 N O9
VQFKFAKEUMHBLV-BYSUZVQFSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0 Å
  • R-Value Free: 0.326
  • R-Value Work: 0.234
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 50.47 α = 90.00
b = 94.30 β = 90.00
c = 176.07 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-05-26
  • Released Date: 2005-07-19
  • Deposition author(s): Koch, M., Stronge, V.S., Shepherd, D., Gadola, S.D., Mathew, B., Ritter, G., Fersht, A.R., Besra, G.S., Schmidt, R.R., Jones, E.Y., Cerundolo, V., Structural Proteomics in Europe (SPINE)

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values