3U0P

Crystal structure of human CD1d-lysophosphatidylcholine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.259
  • R-Value Work: 0.213

Literature

Macromolecules
Sequence Display for 3U0P

Classification: IMMUNE SYSTEM

Total Structure Weight: 138072.72

Macromolecule Entities
Molecule Chains Length Organism Details
Antigen-presenting glycoprotein CD1d A, C, E 284 Homo sapiens Mutation: N42Q, N108Q, N163Q
Gene Name(s): CD1D Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Beta-2-microglobulin B, D, F 102 Homo sapiens Gene Name(s): B2M Gene View CDABP0092 HDCMA22P
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, C (4R,7R,18E)-4,7-dihydroxy-N,N,N-trimethyl- 10-oxo-3,5,9-trioxa-4-phosphaheptacos-18- en-1-aminium 4-oxide
C26 H53 N O7 P
YAMUFBLWGFFICM-ZOGNMOHXSA-O
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

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

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

A UNDECANE
LIPID FRAGMENT (Synonym)
C11 H24
RSJKGSCJYJTIGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A, C, D, F SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A, B, C, D GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
HEX
Query on HEX

A HEXANE
C6 H14
VLKZOEOYAKHREP-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NBU
Query on NBU

E N-BUTANE
C4 H10
IJDNQMDRQITEOD-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
LSC N/A in BindingDB
N/A in BindingMoad
Kd: 2100 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.259
  • R-Value Work: 0.213
  • Space Group: I 2 2 2

Unit Cell:

Length (Å) Angle (°)
a = 108.61 α = 90.00
b = 127.19 β = 90.00
c = 332.64 γ = 90.00

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 2011-09-28
  • Released Date: 2012-04-25
  • Deposition author(s): Lopez-Sagaseta, J., Sibener, L.V., Adams, E.J.

Revision History

  • Version 1_0: 2012-04-25

    Type: Initial release

  • Version 1_1: 2017-11-08

    Type: Advisory, Refinement description