7AW6 | pdb_00007aw6

The extracellular region of CD33 with bound sialoside analogue P22

• PDB DOI: https://doi.org/10.2210/pdb7AW6/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2020-11-06 Released: 2020-12-16 
• Deposition Author(s): Bradshaw, W.J., Katis, V.L., Thompson, A.P., Arrowsmith, C.H., Edwards, A.M., von Delft, F., Bountra, C., Gileadi, O.
• Funding Organization(s): National Institutes of Health/National Institute on Aging (NIH/NIA)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.246 (Depositor), 0.233 (DCC) 
• R-Value Work: 
  0.194 (Depositor) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

The extracellular region of CD33 with bound sialoside analogue P22

Bradshaw, W.J., Katis, V.L., Thompson, A.P., Arrowsmith, C.H., Edwards, A.M., von Delft, F., Bountra, C., Gileadi, O.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 59.99 kDa 
• Atom Count: 3,891 
• Modeled Residue Count: 427 
• Deposited Residue Count: 504 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Myeloid cell surface antigen CD33	A, B	252	Homo sapiens	Mutation(s): 0  Gene Names: CD33, SIGLEC3
UniProt & NIH Common Fund Data Resources
Find proteins for P20138 (Homo sapiens) Explore P20138  Go to UniProtKB:  P20138
PHAROS:  P20138 GTEx:  ENSG00000105383
Glycosylation
Glycosylation Sites: 5		Go to GlyGen: P20138-1

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FVP (Subject of Investigation/LOI)	G [auth A], M [auth B]	2-aminoethyl 5-{[(4-cyclohexyl-1H-1,2,3-triazol-1-yl)acetyl]amino}-3,5,9-trideoxy-9-[(4-hydroxy-3,5-dimethylbenzene-1-carbonyl)amino]-D-glycero-alpha-D-galacto-non-2-ulopyranonosyl-(2->6)-beta-D-galactopyranosyl-(1->4)-beta-D-glucopyranoside C42 H64 N6 O20 DQZXNLDRAKHEEK-XCGJJDHASA-N
NAG	C [auth A], D [auth A], E [auth A], F [auth A], H [auth B], I [auth B], J [auth B], K [auth B], L [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
PO4	N [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO	O [auth B], P [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.246 (Depositor), 0.233 (DCC) 
• R-Value Work:  0.194 (Depositor) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.641	α = 90
b = 103.23	β = 110.42
c = 84.495	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-12-16 
Deposition Author(s): Bradshaw, W.J., Katis, V.L., Thompson, A.P., Arrowsmith, C.H., Edwards, A.M., von Delft, F., Bountra, C., Gileadi, O.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute on Aging (NIH/NIA)	United States	1RF1AG057443

Revision History  

• Version 1.0: 2020-12-16
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary