4ONO

CD1c in complex with PM (phosphomycoketide)

• PDB DOI: https://doi.org/10.2210/pdb4ONO/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2014-01-28 Released: 2014-10-08 
• Deposition Author(s): Roy, S., Adams, E.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.71 Å
• R-Value Free: 0.271 
• R-Value Work: 0.219 
• R-Value Observed: 0.221 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 45.82 kDa 
• Atom Count: 3,069 
• Modelled Residue Count: 374 
• Deposited Residue Count: 395 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin/T-cell surface glycoprotein CD1c/T-cell surface glycoprotein CD1b chimeric protein	A	395	Homo sapiens	Mutation(s): 6  Gene Names: CD1B CD1C B2M CDABP0092 HDCMA22P, CD1C
UniProt & NIH Common Fund Data Resources
Find proteins for P29016 (Homo sapiens) Explore P29016  Go to UniProtKB:  P29016
PHAROS:  P29016 GTEx:  ENSG00000158485
Find proteins for P29017 (Homo sapiens) Explore P29017  Go to UniProtKB:  P29017
PHAROS:  P29017 GTEx:  ENSG00000158481
Find proteins for P61769 (Homo sapiens) Explore P61769  Go to UniProtKB:  P61769
PHAROS:  P61769 GTEx:  ENSG00000166710
UniProt Groups	P29017P29016P61769

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PMK	C [auth A]	(4R,8S,16S,20R)-4,8,12,16,20-pentamethylheptacosyl dihydrogen phosphate C32 H67 O4 P WLNOCCJMGSEDAT-GCIGRYLYSA-N
MLI	J [auth A], K [auth A], L [auth A]	MALONATE ION C3 H2 O4 OFOBLEOULBTSOW-UHFFFAOYSA-L
CL	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.71 Å
• R-Value Free: 0.271 
• R-Value Work: 0.219 
• R-Value Observed: 0.221 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.312	α = 90
b = 86.978	β = 90
c = 89.574	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-10-08 
Deposition Author(s): Roy, S., Adams, E.J.

Revision History  

• Version 1.0: 2014-10-08
  Type: Initial release
  
• Version 1.1: 2015-02-18
  Changes: Database references
• Version 1.2: 2017-07-26
  Changes: Advisory, Data collection, Refinement description, Source and taxonomy
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary