5J0B

Structure of the immune receptor CD33 in complex with 6'-sialyllactose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.231 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

STRUCTURE OF LIGAND BOUND CD33 RECEPTOR ASSOCIATED WITH ALZHEIMER'S DISEASE

Dodd, R.B.Meadows, W.Qamar, S.Johnson, C.M.Kronenberg-Versteeg, D.St George-Hyslop, P.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Myeloid cell surface antigen CD33
A, B, C, D
224Homo sapiensMutation(s): 1 
Gene Names: CD33SIGLEC3
UniProt & NIH Common Fund Data Resources
Find proteins for P20138 (Homo sapiens)
Explore P20138 
Go to UniProtKB:  P20138
PHAROS:  P20138
GTEx:  ENSG00000105383 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20138
Glycosylation
Glycosylation Sites: 3Go to GlyGen: P20138-1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose
E, F, G
2N/A
Glycosylation Resources
GlyTouCan:  G63069TR
GlyCosmos:  G63069TR
GlyGen:  G63069TR
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
H [auth A]
I [auth A]
J [auth A]
K [auth B]
L [auth B]
H [auth A],
I [auth A],
J [auth A],
K [auth B],
L [auth B],
M [auth B],
N [auth C],
O [auth C],
P [auth C],
S [auth D],
T [auth D],
U [auth D]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
PG0
Query on PG0

Download Ideal Coordinates CCD File 
Q [auth C],
R [auth C]
2-(2-METHOXYETHOXY)ETHANOL
C5 H12 O3
SBASXUCJHJRPEV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.231 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.49α = 90
b = 123.68β = 90
c = 141.6γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
XSCALEdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2017-04-05 
  • Deposition Author(s): Dodd, R.B.

Funding OrganizationLocationGrant Number
Wellcome TrustUnited KingdomRG47376

Revision History  (Full details and data files)

  • Version 1.0: 2017-04-05
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary