5EFI

Crystal structure of mouse CD1d in complex with the p99p lipopeptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.244
  • R-Value Work: 0.219

Literature

Macromolecules
Sequence Display for 5EFI

Classification: IMMUNE SYSTEM

Total Structure Weight: 49512.55

Macromolecule Entities
Molecule Chains Length Organism Details
Antigen-presenting glycoprotein CD1d1 A 285 Mus musculus Gene Name(s): Cd1d1 Cd1.1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Beta-2-microglobulin B 99 Mus musculus Gene Name(s): B2m
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
p99p C 22 Mus Details: Palmitate residue covalently linked to Lys 12

Small Molecules
Ligands 8 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
PLM
Query on PLM

C PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

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

A CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MAN
Query on MAN

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

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

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

C OCTANOIC ACID (CAPRYLIC ACID)
C8 H16 O2
WWZKQHOCKIZLMA-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.244
  • R-Value Work: 0.219
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 42.19 α = 90.00
b = 107.85 β = 90.00
c = 110.34 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2015-10-23
  • Released Date: 2016-03-30
  • Deposition author(s): Girardi, E., Wang, J., Zajonc, D.M.

Revision History

  • 2016-04-06
    Type: Database references
  • 2016-06-01
    Type: Database references
  • 2017-09-20
    Type: Author supporting evidence, Database references, Derived calculations